James Hutton Institute

The use of tramlines or wheelings to carry out agricultural operations, such as spraying and fertilizer applications, is common across the world. They are often orientated up and down the slope and the soil that is driven on becomes compacted because of machinery weight transferring stress through the soil profile. This compaction leads to tramlines becoming conduits for water moving over the soil surface. Like water, sediment and phosphorus are also detached and transported. Reducing surface runoff and diffuse pollution losses from surface runoff associated with wheelings has received some research attention, but results are often difficult to interpret. This is because of the low number of replicates that are possible in agricultural landscapes, if the research is to be conducted at meaningful scales and to remain feasible. To address this, we utilize effect sizes and confidence intervals to analyse surface runoff and diffuse pollution data from a series of studies at five arable field sites, in the UK where surface runoff, sediment and phosphorus was collected from hillslope scale tramline plots utilizing the same methodology. In addition, we tested the impact of very flexible tyres, rotary harrows and a surface profiler roller on surface runoff and diffuse pollution loses. Although the monitoring period did not encompass widespread flood inducing storms, we demonstrate that the magnitude of the sediment and total phosphorus (TP) losses from the tramline plots across the study sites are significant in the UK context. Annual sediment losses from the study plots are in the order of 0.5–4.5 Mg ha ⁻¹ yr. ⁻¹ and consistent with the magnitudes of soil erosion in the UK. TP fluxes observed at the study plots, ranged between 0.8 and 3.9 kg ha ⁻¹ yr. ⁻¹ , are consistent with the TP losses reported for surface runoff from arable plots in the UK. By utilizing effect size analysis, we demonstrate the significant impact of tramline mitigation on surface runoff and diffuse pollution losses. The rotary harrow performed best overall, and the combination of the rotary harrow and the very flexible tyre was superior to all other methods. This was the case for all treatments apart from some, where the surface profiler performed well in reducing sediment fluxes. Our work supports the need for incorporating tramline management measures into soil management strategies for arable landscapes and provides evidence for policymakers developing measures for agri‐environmental schemes.

To persist in seasonal environments, animals track, exploit, and store energy when food is plentiful. Seasonal changes in plant phenology that are predictable allow animals to track abundant food resources. However, little is known about how animals use and benefit from ephemeral and unpredictable food pulses during times when food is scarce. Climate change is altering the timing, abundance, and spatial distribution of food releases, emphasizing the ongoing need for understanding how unseasonal weather conditions influence access to food. Using 12 years of GPS‐location data and annual measures of body mass in 72 adult female Svalbard reindeer (Rangifer tarandus platyrhynchus), we tested whether individuals with greater use of nutritionally beneficial resource pulses in autumn and early winter are heavier going into parturition in spring. Additionally, we evaluated how stochastic weather conditions influence the use of food resources. Reindeer that foraged most in marshes during autumn and early winter gained a positive carryover effect of up to 5 kg heavier body mass in late winter, with previously demonstrated benefits to both survival and reproduction. Marsh use was rare, brief, and intense, which is the expected response to a pulsed resource. The extent to which marshes were used varied greatly among years and was associated with stochastic mild spells that relaxed constraints of snow depth for a few days. Compared with other habitats used, marshes offered superior quantity and quality of belowground plant biomass that may be accessed more easily under milder autumn and winter conditions. Our findings demonstrate the individual benefits of exploiting stochastic food pulses and showcase how resource tracking during periods of food scarcity may be a behavioral trait that could enhance population resilience in a rapidly warming climate.

Potato virus Y (PVY, genus Potyvirus, family Potyviridae) is one of the most devastating and economically important potato pathogens. Members of the Potyviridae family demonstrate high recombination rates. In nature, 5 major parental variants of PVY were identified with at least 35 recombinants. In this study we report two novel PVY recombinants discovered in the sprouts of potato tubers produced in field conditions in Astrakhan region of Russia in 2021 using high-throughput sequencing and de novo genome assembly. These recombinants, which were named Ast-A-I and Ast-A-II, have previously unknown arrangements of genome sections derived from PVYO and PVYN with a novel recombination junction at the position 7850 nt of the PVY genome, in the middle part of the RNA-dependent RNA polymerase (NIb) gene, with PVYO-type sequence at the 5’-end of this junction and PVYN-type at the 3’-end. Other recombinant junctions in the novel PVY variants were previously found in PVYNTNa and PVYNTNb. This includes those at the positions 2390 and 9200 (PVYN at the 5’-end and PVYO at the 3’-end) which were present in both novel recombinants, and at the position 500 (PVYO at the 5’-end and PVYN at the 3’-end) which present in Ast-A-II. The presence of PVY variants with novel recombinant point is verified by Sanger sequencing. Phylogenetic analysis of genomic RNA showed that the sequences of these recombinants form a separate branch which do not cluster with previously described PVY strains.

There is an urgent need for woodland expansion to help enhance and restore vital forest ecosystem services. However, the process of natural regeneration of woodlands is often slow, requiring active reforestation approaches. Factors limiting regeneration are complex, but there is increasing evidence that natural woodland expansion onto sites that have been treeless for a long period of time may be limited by the loss of microbial woodland‐soil properties. This study explored a potential role for mycorrhizal associations in facilitating obligate ectomycorrhizal (ECM) tree establishment, with potential implications for active reforestation practices. We determined the spatial distribution patterns of ECM tree seedlings – Pinus sylvestris and Betula spp. – outwith a woodland, in relation to existing dual‐mycorrhizal Salix plants. There was very strong evidence that ECM tree seedlings were more likely to be found growing within groups around Salix than as isolated individuals, supporting the view that Salix drives the current spatial distribution patterns of ECM tree establishment. We suggest that the ability of Salix to form dual AM and ECM associations allows it to become established across the open AM dominated vegetation. Over time these plants become colonised by ECM fungi via aerial spores and then can act as a source of inoculum for obligate ECM tree seedlings, which arrive as seeds in the vicinity of Salix . This study highlights the potential role of dual‐mycorrhizal Salix as a nurse plant in supporting secondary forest succession of obligate ECM boreal/temperate woodland species onto adjacent open areas through nucleation. Overall, we concluded that there is potential for existing ECM networks to aid tree establishment and propose a nature‐based approach to maximize reforestation efforts by targeting existing symbiotic fungal networks as nucleation points for tree planting. Our findings contribute to understanding the ecological dynamics involved in woodland expansion and restoration.

Marine microalgae demonstrate a notable capacity to adapt to high CO2 and warming in the context of global change. However, the dynamics of their evolutionary processes under simultaneous high CO₂ and warming conditions remain poorly understood. Here, we analyze the dynamics of evolution in experimental populations of a model marine diatom Phaeodactylum tricornutum. We conducted whole‐genome resequencing of populations under ambient, high‐CO2, warming and high CO2 + warming at 2‐yr intervals over a 4‐yr adaptation period. The common genes selected between 2‐ and 4‐yr adaptation were found to be involved in protein ubiquitination and degradation and the tricarboxylic acid (TCA) cycle, and were consistently selected regardless of the experimental conditions or adaptation duration. The unique genes selected only by 4‐yr adaptation function in respiration, fatty acid, and amino acid metabolism, facilitating adaptation to prolonged high CO2 with warming conditions. Corresponding changes at the metabolomic level, with significant alterations in metabolites abundances involved in these pathways, support the genomic findings. Our study, integrating genomic and metabolomic data, demonstrates that long‐term adaptation of microalgae to high CO2 and/or warming can be characterized by a complex and dynamic genetic process and may advance our understanding of microalgae adaptation to global change.

Soil forensics is not only a well‐established research domain but has also been used in numerous successful international searches for burials and as trace evidence to help police and law enforcement in solving criminal, environmental and terrorism investigations. However, despite the confidentiality and legal constraints in case work in many parts of the world, some actual case studies using soil materials as evidence in court hearings have been published in international journals and books. This paper presents a case from the Campania region in Italy where soil analysis played a pivotal role. Employing a multiscale integrated approach encompassing soil microtomography, morphology, chemical analysis and geography, the study aimed to discern the origin of questioned soil residues found on a victim of crime. Results highlight the significance of considering spatial variability and an appropriate choice of analytical methods. The sequential and multiscale approach facilitated timely investigation without incurring unnecessary costs. Soil morphological and chemical analysis revealed inconsistencies between soil on the victim and soil at the suspected crime scenes, narrowing the investigative area down to approximately one square km. While detailed sampling did not yield statistically significant results, the evidence provided crucial insights, aiding investigators in working out what happened and helped in building a narrative around their case. The analysis indicated contact with a primary scene where the victim was likely dragged (over a Calcisol) and a final deposition site (over an Andosol) where the body was found. While potential murder sites were excluded, final guilt attribution remained inconclusive, and as in all trace evidence evaluation, it is not the role of the forensic soil scientist to consider the level of guilt, but to provide factual soil forensic evidence to assist the justice system. This study exemplifies the use of soil forensics in informing criminal investigations and highlights the complexities that can be involved in establishing comparability between soil samples.

We urgently need to foster regenerative food systems that mutually reinforce human and ecological health. However, we have limited understanding of the action pathways that could encourage the emergence of such systems. Here we report on an extensive Three Horizons futures process, conducted with diverse participation from food system researchers and practitioners, to identify core domains of action for transforming the food system of Yorkshire, UK, towards a regenerative future. After establishing the contrast between the current degenerative and envisioned future regenerative food system, six core action domains were identified that require support to enable transformation: 1) enhancing supply chain connectivity and innovation to support diverse hybrid business ecosystems; 2) scaling environmentally beneficial and regenerative farming; 3) empowering citizens to reshape food demand; 4) providing trusted, accessible knowledge support for standards and incentives; 5) supporting schools and young people as drivers of long-term change; and 6) ensuring coordination and mutual support across domains. Our results highlight the importance of efforts to cohere synergic action, ambitious visioning, and addressing issues of power. Overall, our study sets an ambitious standard for co-developing action priorities to encourage regenerative futures.

Land management by seasonal migratory herding, traditionally implemented by pastoralists, has allowed semi-arid rangeland ecosystems to remain productive and resilient to highly erratic, seasonal rainfall patterns. Changing pastoralist practices and rainfall patterns due to climate change have the potential to negatively influence the resilience of rangelands. To test the impact of different communal rangeland practices and increasing frequency of disturbance on the rangelands’ vegetation, we established a clipping experiment in three rangeland management types: rainy season rangeland, dry season rangeland and seasonal exclosures, in the Maasai Steppe, northern Tanzania. Across these rangeland management types, we tested two clipping frequencies monthly vs. once per growing period and either fenced or open to grazing (herbivory) over two consecutive growing periods. We found that rainy season rangeland exhibited lowest regrowth rates and highest proportion of bare ground across herbivory, clipping frequency and growing period. When rainfall was low, seasonal exclosures showed lowest proportion of bare ground across herbivory and clipping frequency and plots that were seasonally clipped and excluded herbivores generated significantly more grass biomass, higher grass regrowth rates and lowest proportion of bare ground compared to all other treatments. Excluding herbivores had little impact on the vegetation biomass and cover but had a positive impact on grass regrowth rates when rainfall was high. Seasonal clipping allowed for lower proportion of bare ground, and in most cases higher regrowth rates and higher biomass compared to monthly clipping. We conclude that traditional seasonal migratory herding is a relevant concept to sustain rangeland productivity and resilience under increasing intensity of disturbance if grazing pressure on rainy season rangelands is adapted to rainfall conditions and sufficient resting time after heavy defoliation is granted. Dry season grazing (including rainy season resting) proved to be the most sustainable concept to maintain regrowth and control erosion.

In this study, we define, categorize, and systematically describe best practices and barriers to implementing preference elicitation lab‐in‐the‐field experiments with farmers based on qualitative, in‐depth interviews with researchers from the Research Network on Economic Experiments for the Common Agricultural Policy (REECAP). Following an assessment of the challenges the researchers faced and the solutions they adopted, we provide a step‐by‐step guide to conducting such experiments. We elaborate on limitations and provide recommendations and suggestions for future research.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species¹. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants². Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.

Background Compatibility between plant parasites and their hosts is genetically determined {Citation}both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes. Results We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 (Resistance to Acyrthosiphon pisum 1) resistance quantitative trait locus. Differential gene expression analysis of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence or avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some genes were differentially expressed both in the transcriptome and in the proteome datasets, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (27%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered. Conclusions Especially when combined with tightly controlled genetics of both insect and host plant, multi-omics approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.

A plausible, but largely unexplored reason for many weed biocontrol agents failing to establish or being ineffective, could involve abiotically induced changes to an invasive plants’ biochemical phenotype and consequent enhanced herbivore resistance. Considerable literature demonstrates that chemically altered plant phenotypes can impair insect life history performance. Heather beetle, (Lochmaea suturalis), introduced to control invasive heather (Calluna vulgaris) in New Zealand (NZ) was difficult to establish and displays variable effectiveness. Using UHPLC-MS non-targeted metabolomics, we analysed primary and secondary metabolites of C. vulgaris from its native range (Scotland) and it’s introduced range (NZ), between which, differences in soil nutrients and ultraviolet light exist. We also explored secondary metabolite variation between sites within each range. New Zealand samples had the highest number of amplified metabolites, most notably defensive phenylpropanoids, supporting the concept of abiotically induced upregulation of key biosynthetic pathways. Analysis of secondary metabolite variation within each range revealed differences between sites but found little correlation of phenylpropanoid levels being influenced by variable soil nutrients. These results validate questions about the possibility of abiotically altered biochemical phenotypes in invasive plants, influencing weed biocontrol agent establishment and effectiveness, and show the potential for metabolomics in assisting future, or retrospectively analysing biological control programmes.

Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome’s 3D chromosomal folding.

‘New economics’ discourses – comprising diverse approaches advocated as more just and sustainable replacements of dominant neoclassical and neoliberal economic perspectives – have been criticised as insufficiently coherent to form the ‘discourse coalitions’ necessary to enter the mainstream. To date there has been little systematic exploration of the agreement or divergence in new economics discourses. Here, we conduct a qualitative systematised review of new economics literature in the context of the COVID-19 pandemic to analyse stances towards the economic status quo and the depth of change advocated in it, such as fundamental and systemic transformation or more superficial reformist or accepting types of change that mostly maintain current economic systems. We interpreted authors’ stances towards six key status quo themes: capitalism; neoliberalism; GDP-based economic growth; debt-based money; globalisation; and the Sustainable Development Goals (SDGs). In the 525 documents analysed, there was relative consensus that neoliberalism needed transforming, stances towards GDP-based growth substantially diverged (from transformative to reformist/accepting), and stances towards the SDGs were mostly accepting, although the status quo themes tended to be infrequently mentioned overall. Different new economics approaches were associated with diverging stances. We suggest that alignment against neoliberalism and towards the SDGs may provide strategic coalescing points for new economics. Because stances towards core problematised aspects of mainstream economics were often not articulated, we encourage new economics scholars and practitioners to remain explicit, aware and reflexive with regard to the economic status quo, as well as strategic in their approach to seeking economic transformation.

Pastoralism is gaining in recognition for its provision of a broad range of ecosystem services. However, in Western countries, especially in Europe, it has been in decline for decades and its future is uncertain. Professional satisfaction, social appreciation and community integration are key factors for the sustainability of any activity. Using information from 167 traditional Spanish herders, we assessed their perceived degree of satisfaction with their profession and the reasons behind their perceptions. Herders were extremely satisfied with their profession, but they perceived medium and low levels of appreciation by the rural and urban sectors of society, respectively. Herders had negative feelings about the sustainability of their profession, as they felt more appreciated by society in the past than they do today, half of them did not want their offspring to make a living as herders. Improving communication between herders and society could help to enhance herders’ appreciation of their profession. Graphical abstract