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Final Report for Stapledon Memorial Trust Fellowship
No full textGreenhouse gas emissions(GHG) from the agricultural sector are a major concern. One of the most potent GHG is Nitrous Oxide (N20), which around 60% of the emissions comes from the agricultural soils. The N20 production depends on many variables, such us WFPS, temperature, pH, management, Carbon and Nitrogen content. In this experiment we are going to study the effect of soil management, the dynamic and interaction between C and N in the N2O emissions from soils of a long-term experiment of Uruguay.
Soils has been 60 years under different managements, for the study we select (from 7 treatments) 2 rotations: 1- CA continuous agriculture, from a typical crop rotation in Uruguay; and 2-CP the same crop rotation with 50 % of the time with pasture. Soils were sampled in June 2024 and sent to the UK to do an incubation in the Denitrification system at Rothamsted Research in Devon. To study the effect of the different carbon content because of different crop rotation in the emissions
Adaptations in agricultural water management in arid regions: Modelling farmer behaviour and cooperation on irrigation sustainability in Morocco
No full textClimate change has disrupted weather patterns and heightened drought risks in arid and semi-arid regions, requiring adaptations to crop and irrigation strategies to sustain food production. This study integrates qualitative and quantitative approaches to examine the factors influencing farmers crop and irrigation management decisions, with a focus on groundwater management and drip irrigation adoption. Semi-structured interviews 70 farmers from Al Haouz Basin, Morocco provided insights into motivations for crop and irrigation choices. Inductive coding was used for qualitative responses, and data analysis examined how farm size and tenure influenced decision-making. An integrated modelling approach combining the theory of planned behaviour and structural equation modelling (SEM) was used to interpret drivers of irrigation management strategy. The interviews revealed that 83 % of farmers were concerned about groundwater decline, with 40 % identifying salinity as a major challenge. We found that falling groundwater levels and soil salinization have already impacted yields and raised concerns about further declines, prompting large-scale farmers to transition to more profitable and drought-resilient olive cultivation. Analysis of the SEM showed that attitudes toward drip irrigation efficiency, maintaining groundwater supply, and preventing increases in groundwater salinity influence farmers’ intentions regarding their water usage. Additionally, perceived behavioural control played a key role in shaping adoption behaviours, reinforcing the importance of structural and economic factors in decision-making. Land ownership conferred greater long-term perceived control over sustainable water use. However, qualitative findings revealed that cooperation on groundwater management was limited, with many farmers citing a lack of perceived benefits and logistical challenges, highlighting collective action challenges. Complexities related to subsidy applications and land tenure deter drip irrigation adoption, especially among smallholders, constraining climate change resilience. Our study contributes to understanding farmers' coping strategies and presents a foundation from which to develop evidence-based policy reforms enhancing agricultural and water sustainability across arid and semi-arid regions
Importance of dietary fibre, strategies for increasing intake and maintenance of the supply chain in the UK
No full textCurrently, dietary fibre intakes within UK populations are far below those recommended for reducing chronic disease risk. Dietary fibre is present predominantly in plant-based foods and is not digested or absorbed in the upper gastrointestinal tract, passing to the colon where it may be fermented by the gut microbiota. Types, contents and properties (notably solubility, viscosity and fermentability) of fibre vary considerably between food sources, which may result in different effects on human physiology. There is strong evidence for the benefits of dietary fibre, particularly cereal fibre and wholegrain, in reducing the risk of cardiometabolic diseases and colorectal cancer by increasing faecal mass, fermentation to short-chain fatty acids, lowering blood lipids and improving glycaemic control. There is, therefore, an urgent need to develop effective strategies to increase the intake of dietary fibre across the UK population. Here, we consider strategies comprising better nutritional education, public health messaging, more informative and effective food labelling, food reformulation, food fortification and biofortification, policy change and maintenance of the supply chain. Engagement of multiple stakeholders within the food system in this common ambition is essential for success. This requires transformation of the UK food system to ensure the sustainable availability of palatable, affordable, fibre-rich foods, ideally accompanied by individual motivation for dietary change.
This article is part of the theme issue ‘Transforming terrestrial food systems for human and planetary health’
Integrating leaf scaled spectra and machine learning for rapid estimation of photosynthetic phenotypes across soybean genotypes
No full textPhotosynthesis is central to crop productivity and global carbon dynamics, yet traditional methods for evaluating
photosynthetic capacity are slow, low-throughput, and difficult to scale. This study presents a novel, rapid, nondestructive approach to estimate soybean leaf photosynthetic phenotypes using hyperspectral reflectance and machine learning. A new index, the comprehensive photosynthetic phenotype indicator (CPPI), was developed using principal component analysis to integrate gas exchange, chlorophyll fluorescence, and pigment traits into a single predictive variable. To achieve rapid estimation of soybean leaf photosynthetic phenotypes, leaf-scaled hyperspectral data along with photosynthetic indicators, fluorescence parameters, and pigments across 62 soybean genotypes over two growing seasons and three growth stages were collected. Three machine learning methods combined with transformed spectra were used to test the predictive performance for soybean photosynthetic phenotypes. The results showed that the developed CPPI achieved strong predictive performance (R2v= 0.704, RMSE = 0.779, RPD = 1.838), comparable to the best single trait of Trmmol (R2 v = 0.793, RMSE = 1.827, RPD = 2.012). These key spectral regions or wavelengths of 350–380, 550, 680–750, 860, 1390, 1660, and 1710 nm contributed to the spectral prediction as they are highly and secondarily related to leaf photosynthetic phenotypes. Moreover, it was found that spectral pretreatment offered limited improvement to the spectral model performance, while integrating partial least squares (PLS) regression with selected informative wavelengths enhanced prediction stability and robustness. Our results demonstrate the potential of CPPI as a scalable, integrative trait for high-throughput phenotyping and breeding applications. This approach allows for rapid screening of high-efficiency photosynthetic genotypes under field conditions, offering a practical tool for improving crop productivity through spectral selection
Bacterial Composition of Meloidogyne exigua Egg Masses from Symptomatic and Asymptomatic Coffee Plants
No full textRoot-knot nematodes (Meloidogyne spp.) threaten global agricultural production. Bacteria that inhabit the nematode egg mass have not been well explored. Using a metataxonomic approach based on sequencing the 16S rRNA gene of bacteria communities associated with Meloidogyne exigua egg masses, we found significant differences in bacterial composition and diversity in the egg masses of symptomatic coffee plants compared with asymptomatic ones for the first time in field conditions. The families Pseudomonadaceae, Burkholderiaceae, Flavobacteriaceae, Rhizobiaceae, Micrococcaceae, and Bacteroidaceae were more abundant in egg masses sampled from asymptomatic plants, and Chitinophagaceae, Glycomycetaceae, Micropepsaceae, Beijerinckiaceae, and Enterococcaceae were more abundant in samples from symptomatic plants. The genera Pseudomonas, Sphingobacterium, Flavobacterium, Corynebacterium, and Virgibacillus were found in greater abundance in egg masses from asymptomatic plants, and only Tumebacillus and Bacillus were significantly more abundant in samples from symptomatic plants. The reproduction and infectivity of M. exigua was tested in tomato plants. The reproduction index of M. exigua (nematodes eggs per gram of roots) was significantly lower when applying nematode inocula from asymptomatic coffee plants compared with inocula from symptomatic plants. The root weight of tomato plants infected with inocula from asymptomatic coffee plants was significantly higher than that of plants infected with inocula from symptomatic plants. However, there was no significant difference in the infectivity index (number of galls per root system) of tomato plants when inoculated with inocula from either source (P ≤ 0.05). This study showed a differential bacterial community colonizing coffee plants with different levels of nematode infections, which opens the door for future nematode biological control
Animal and pasture responses in contrasting temperate pasture-based cattle management systems: set-stocking versus cell grazing
No full textGrasslands cover a significant portion of the Earth's land and offer many benefits. In the UK, they constitute the largest agricultural area and support livestock production. Traditional set-stocking (SS) and continuous grazing methods allow animals to selectively graze more palatable and nutritious plant parts and species, boosting individual animal productivity in the short-term but can be detrimental to long-term pasture productivity. Cell grazing (CG), an intensive rotational system, is proposed as an alternative that can enhance system productivity and profitability through increased pasture production, utilization, and stocking rates; with potential to optimise natural resource use (e.g., land) and mitigate environmental impacts (e.g., soil carbon sequestration). A four-year study at Rothamsted Research’s North Wyke site in southwest England compared animal and pasture responses under SS and CG stocking methods using a split-block design with three replicates (enclosures) per treatment. The SS enclosures (1.5-1.75 ha) were continuously grazed with fixed stocking rates and CG enclosures (1.0 ha) were rotationally grazed with flexible daily grazing area allocations and stocking rates. Grazing occurred spring to autumn, using two cohorts of autumn-born dairy × beef steers, each grazed for two years before slaughter. Measurements included standing herbage mass (weekly), herbage chemical composition (fortnightly), steer liveweight (monthly), and botanical composition (spring 2018 and 2022). Dry matter intake was estimated based on animal energy requirements. Significant interaction effects (p<0.05) were found for most variables, apart from metabolizable energy, ADF and NDF which were affected by treatment (p<0.05) and year (p<0.001), and DM content which was affected by year only (p<0.001). Average daily gain was higher in SS (0.77 kg/d) than CG (0.60 kg/d), linked to higher estimated DM intake (7.2 vs. 6.2 kg DM). However, annual liveweight (LW) production per hectare was greater in CG (687 vs. 476 kg LW/ha, respectively), due to higher total pasture production (6 053 vs. 3 667 kg DM/ha, respectively) and stocking rate (2 362 vs. 1 290 kg LW/ha, respectively). Herbage nutritional quality varied, with CG having higher metabolizable energy and water-soluble carbohydrates, and lower fibre (ADF and NDF) concentrations. Changes in botanical composition also varied between treatments. The proportion of perennial ryegrass increased under CG (42% to 69%, p<0.001) but declined under SS (36% to 16%, p<0.01). These results highlight that while SS can enhance individual animal gains, CG improves total system productivity and pasture composition. Long-term, replicated experiments like this are crucial for evaluating the long-term viability and sustainability of differing stocking methods and grazing management strategies
Long-term manure and mineral fertilisation drive distinct pathways of soil organic nitrogen decomposition: Insights from a 180-year-old study
No full textSoil organic nitrogen (SON) decomposition is a fundamental process in the nitrogen (N) cycle that influences N
availability for plant uptake and soil health. However, the long-term effects of nutrient fertilisation on SON decomposition and its microbial drivers remain poorly understood. Here, we used the 180-year-old Broadbalk Winter Wheat Experiment to investigate how farmyard manure (FYM), mineral fertiliser (NPK), and no fertilisation input (NIL) affect crop yield, SON turnover, microbial community composition, and functional genes. Our findings showed that distinct and complementary microbial mechanisms regulate SON decomposition under different nutrient fertilisation treatments. FYM application increased gross N mineralisation to 43.1 mg N kg− 1 soil d− 1, by doubling microbial biomass and promoting bacterial-dominated protein and peptide decomposition. During the early stage of decomposition, CO2 release from protein and peptide turnover under FYM increased by 96 % and 44 %, respectively, compared to NIL. NPK fertilisation enhanced the decomposition of complex N compounds and promoted the turnover of high-molecular-weight N to support microbial growth by upregulating N-cycling genes and extracellular enzyme production. The carbon use efficiency of protein was increased to 0.68. NPK fertilisation also stimulated fungal and Actinobacteria populations, accelerating the turnover rate of peptides and amino acids to 22.7 and 2.4 mg N kg− 1 soil d− 1, respectively. These results provide new insights into how nutrient fertilisation practices affect microbialy-mediated N dynamics and crop productivity, emphasising the importance of microbial functional diversity in supporting soil N cycling and fertility
Revisiting the Evolution and Function of NIP2 Paralogues in the Rhynchosporium Spp. Complex
No full textThe fungus Rhynchosporium commune, the causal agent of barley scald disease, contains a paralogous effector gene family called Necrosis-Inducing Protein 2 (NIP2) and NIP2-like protein (NLP). However, the function and full genomic context of these paralogues remain uncharacterised. Here we present a highly contiguous long-read assembly of a newly isolated Australian strain, R. commune WAI453, that is virulent on multiple barley cultivars. Using this assembly, we show that the duplication of the NIP2 and NLP gene families is distributed throughout the genome and pre-dates the speciation of R. commune from other species in the Rhynchosporium genus. Some NIP2 paralogues have subsequently been lost or are absent in these closely related species. The diversity of these paralogues was examined from R. commune global populations and their expression was analysed during in planta and in vitro growth to evaluate the importance of these genes during infection. The majority of NIP2 and NLP paralogues in the WAI453 genome were significantly upregulated during plant infection suggesting that the NIP2 and NLP genes harbour virulence roles. An attempt to further characterise the function of NIP2.1 by infiltrating purified protein into barley leaves did not induce necrosis, questioning its previously reported role as an inducer of host cell death. Together these results suggest that the NIP2 effector family does play a role during infection of barley; however, the exact function of NIP2, like many effectors, remains uncharacterised
Membrane-permeable trehalose 6-phosphate precursor spray increases wheat yields in field trials
No full textTrehalose 6-phosphate (T6P) is an endogenous sugar signal in plants that promotes growth, yet it cannot be introduced directly into crops or fully genetically controlled. Here we show that wheat yields were improved using a timed microdose of a plant-permeable, sunlight-activated T6P signaling precursor, DMNB-T6P, under a variety of agricultural conditions. Under both well-watered and water-stressed conditions over 4 years, DMNB-T6P stimulated yield of three elite varieties. Yield increases were an order of magnitude larger than average annual genetic gains of breeding programs and occurred without additional water or fertilizer. Mechanistic analyses reveal that these benefits arise from increased CO2 fixation and linear electron flow (‘source’) as well as from increased starchy endosperm volume, enhanced grain sieve tube development and upregulation of genes for starch, amino acid and protein synthesis (‘sink’). These data demonstrate a step-change, scalable technology with net benefit to the environment that could provide sustainable yield improvements of diverse staple cereal crop
Herbivore-Plant-Soil microbe interaction: Who is helping whom?
No full textPlant-microbe interactions are key to improving plant defence against herbivory which causes significant losses in food production worldwide. This project aimed to study how aphid herbivory changes the chemical signalling at the plant-soil microbe interface, and to disentangle the complexity of these interactions using a multidisciplinary approach involving microbiology, chemical ecology and bioinformatics.
In an initial experiment where wheat plants were exposed to aphid herbivory for two weeks, rhizosphere bacterial diversity was observed to decrease, with an increased the relative abundance of Actinobacteria class (p < 0.05). Furthermore, untargeted metabolomics analyses showed that the profile of volatile organic compounds (VOCs) in the rhizosphere soil was significantly different under herbivory (p < 0.05). Based on these findings, a second experiment was design using a semi-hydroponic system to facilitate the analysis of chemical signals released by plants via root exudates and volatile organic compounds. Furthermore, rhizosphere and root tissue collection were performed for DNA extraction and amplicon sequencing analysis (16S rRNA). The metabolomics analysis showed that aphid herbivory induced significant changes in the root exudate profile, with 485 metabolites altered and 39 compounds significantly enriched under herbivory. Chemical classification revealed that some of these compounds belong to the benzoxazinoids, terpenes, coumarins and flavonoid classes of secondary metabolites, with some – like HMBOA – previously identified as key signals in plant-microbe interactions under herbivory. In contrast, herbivory resulted in the depletion of certain oxidised fatty acids and amino acids in root exudates. Amplicon sequencing revealed that, some Actinobacteria genera found in the initial experiment (Streptacidiphilus, Streptomyces, Catenulispora), were enriched in the roots of plants under herbivory. Further investigations demonstrated that four herbivory-regulated compounds influenced the growth of rhizosphere bacteria isolated from wheat rhizosphere, suggesting that these metabolites play a functional role in shaping plant-microbe interactions.
Overall, this work shows that aboveground insect pests can have a significant impact on plant belowground interactions, and further research is needed to investigate how to use this knowledge for the development of sustainable pest management strategies that put the soil microbial communities at the centre of crop production