James Hutton Institute
  • Aberdeen, United Kingdom
Recent publications
Forest expansion can make an important contribution to the 2015 Paris Agreement, through offsetting Greenhouse gas (GHG) emissions. EU, UK and Scottish forest policy encourages substantial forest expansion. Unfortunately, policy is still inadequately informed by high resolution data, and often assumes a fairly homogenous landscape, uniformly suitable soil types and idealised ‘average’ tree timber yields, while carbon emissions caused by soil disturbance during planting, and changes in climate are rarely adequately considered. Also, the proportional contribution of afforestation targets to national mitigation needs is often overlooked which could lead to over-reliance on tree planting. We address these shortcomings through an integrated modelling approach which estimates net carbon gain for eleven tree species accounting for the interactions between climate, soil and planting practices. We present detailed spatial results for a case study area (Scotland), showing where forest expansion would be likely to result in overall carbon gains, accounting for the differentiated spatial variability of timber yield classes for each one of the species considered including present and future climate. The results showed that upland ecosystems, whose soils are rich in carbon, were vulnerable to net carbon loss, particularly with intensive ground preparation and planting practices. While the prevalence of mineral soils in the lowlands makes them a safer option for planting in theory, these are also areas which might conflict with agricultural activities. Our findings strongly support the notion that both “the right tree in the right place” and “no trees in the wrong place” are important messages for practitioners. In terms of the total UK and Scottish carbon footprints, the magnitude of the offset obtained in 30 years if afforestation goals were fully reached would likely be around 1% of the UK total business as usual GHG footprint and around 10% of the Scottish footprint. Our results can help to improve the targeting of incentives and investments in forest and woodland expansion, but also reinforce the need to pursue emissions reductions in a variety of ways throughout all sectors.
Accurate predictions of land-use change are important for supporting planning. Cellular automata (CA) models are widely used to simulate real-world urban land-use change but accurately modeling complex spatial urban patterns and dynamics can be challenging due to the high degree of subjectivity involved in CA model parameterisation. Advances in deep learning enable complex spatial patterns such as urban development to be learned and simulated. In this study, we used the U-Net deep learning algorithm to capture historical urban development and simulate future patterns for the North China Plain, one of the most rapidly urbanizing regions on the planet. We validated the model against a reference map for 2018 then applied it in predicting patterns of urban expansion for 2030. The results showed that U-Net can accurately predict urban land-use and mimic real-world spatial patterns with very low requirement for model parameterization and forcing data. Visual inspection of the outputs revealed that U-Net was able to automatically learn complex urban development patterns and processes such as neighborhood influence, the gravity effects of large cities, and the tendency for linear development. Deep learning architectures such as U-Net provide a new parameter-free way to accurately capture and simulate spatial features in projections of future urban development and land-use change.
The roots of most terrestrial plants form symbioses with a diversity of arbuscular mycorrhizal (AM) fungi, which make substantial contributions to plant phosphorus (P) uptake. Large genetic variation exists within AM fungi of the same species. However, the impact of these variations, on the mycorrhizal contribution to plants' P uptake by different isolates of the same species and the differences in physiological mechanism remain unknown. In the present study, we selected maize (genotype Oh 43) as the host plant and investigated the response of plant P uptake and soil organic P use efficiency to two different AM fungal isolates, Rhizophagus irregularis MUCL 41833 and R. irregularis MUCL 43194 at three soil P availability levels (10.3, 18.6, 43.3 mg kg⁻¹, representing low, medium and high soil available P level, respectively). We found that at the medium soil available P level, R. irregularis MUCL 41833 produced large amounts of extraradical hyphae to explore soil and induced greater expression of phosphate transporter gene ZmPHT1;6 involved in the mycorrhizal pathway. While, R. irregularis MUCL 43194 recruited a specific, and different, bacterial community in the rhizosphere compared to R. irregularis MUCL 41833. This shift in rhizosphere microbiome was characterized by the recruitment of a greater abundance of Betaproteobacteriales when the plant was colonized by R. irregularis MUCL 43194, which showed a strong positive correlation with alkaline phosphatase activity, and suggested a link to greater organic P mineralization. Collectively, our results suggest that the two isolates of R. irregularis have different strategies for improving plant P uptake at the medium soil available P level, which deepened our understanding on the contribution and complexity of the mycorrhizal pathway to plant P uptake.
The remediation of legacy metal(loid) contaminated soils in-situ relies on the addition of [organic] amendments to reduce the mobility and bioavailability of metal(loid)s, improve soil geochemical parameters and restore vegetation growth. Two vermicomposts of food and animal manure waste origin (V1 and V2) were amended to an arsenic (As) and copper (Cu) contaminated mine soil (≤1500 mg kg⁻¹). Leaching columns and pot experiments evaluated copper and arsenic in soil pore waters, as well as pH, dissolved organic carbon (DOC) and phosphate (PO4³⁻) concentrations. The uptake of As and Cu to ryegrass was also measured via the pot experiment, whilst recovered biochars from the column leaching test were measured for metal sorption at the termination of leaching. Vermicompost amendment to soil facilitated ryegrass growth which was entirely absent from the untreated soil in the pot test. All amendment combinations raised pore water pH by ∼4 units. Copper concentrations in pore waters from columns and pots showed steep reductions (∼1 mg L⁻¹), as a result of V1 & V2 compared to untreated soil (∼500 mg L⁻¹). Combined with an increase in DOC and PO4³⁻, As was mobilised an order of magnitude by V1. Biochar furthest reduced Cu in pore waters from the columns to <0.1 mg L⁻¹, as a result of surface sorption. The results of this study indicate that biochar can restrict the mobility of Cu from a contaminated mine soil after other amendment interventions have been used to promote revegetation. However, the case of As, biochar cannot counter the profound impact of vermicompost on arsenic mobility.
We report a novel approach for establishing the number and position of CO events in individual homozygous inbred plants by combining low level EMS mutagenesis, speed breeding, whole genome shotgun sequencing and sliding window analysis of the induced molecular variant data. We demonstrate the approach by exploring CO frequency and distribution in self-fertilised progeny of the inbred barley cultivar Bowman and compare these observations to similar data obtained from a Bowman nearly isogenic line (BW230 Hvmlh3) containing a mutation in the DNA mismatch repair gene HvMLH3. We have previously shown that Hvmlh3 decreases both plant fertility and recombination by ~50%. We compare our results to those from previously published traditional genetic analysis of F3 families derived from multiple F2 lines containing WT or mutant alleles of HvMLH3, revealing a high level of correspondence between analyses. We discuss possible applications of the approach in streamlining the assessment of recombination in plant meiosis research.
Social media impact not only our communication and social interactions but also our relationships to the natural environment. Social media can increase understanding of our environment by offering information and sharing calls to action, while at the same time, they might present a glamourised, standardised picture of nature and distract from actual outdoor interactions. The COVID‐19 pandemic presents a unique opportunity to study the spaces created for interactions between the online and offline natural world, especially in countries where movement and thus outdoor activities were restricted during lockdowns. To understand these interactions, we investigated the social media communication of nature conservation and outdoor organisations by analysing Twitter posts of four prominent NGOs in Scotland. We found that during the first COVID‐19‐induced UK lockdown in spring 2020, Scottish nature conservation and outdoor organisations made distinctive efforts in supporting followers to connect with nature in the face of restrictions. Organisations showed signs of moving towards community‐building through sharing experiences often related to nearby nature, while calls for environmental action, more prominent in the previous year, receded in relative importance. Emphasis was put on sensory engagement with, and finding solace in the rhythm of, nature. References to taking action to protect nature now became linked to a green recovery from the pandemic. We conclude that NGOs used social media not as a space separate from the outdoors, but as an augmented space where online and offline interactions were interwoven and a space in which during the COVID‐19 pandemic, new avenues for engagement were being explored. Read the free Plain Language Summary for this article on the Journal blog. Read the free Plain Language Summary for this article on the Journal blog.
BACKGROUND: Berry pomaces obtained after commercial juice production contain phytochemicals which may find use as antioxidants, food additives and biomedical products. Oil extraction from seeds provides additional value but the availability of phytochemicals before and after oil extraction is not well established. OBJECTIVE: This pilot study defines the content and composition of phytochemicals from raspberry and black currant pomaces after extraction with water-ethanol mixes, but also before and after milling/ oil extraction. METHODS: The total phenol (TPC), total anthocyanin (TAC) and antioxidant content of extracts was assessed. Their phytochemical composition was studied using liquid chromatography-mass spectrometry (LC-MSn). RESULTS: TPC and TAC increased with increasing % ethanol. Anthocyanins were major components in blackcurrant pomace and were more readily extracted than total phenols. Total oil content and composition was not influenced by solvent pre-extraction. Milling/ oil extraction markedly increased TPC from raspberry but not from blackcurrant pomace. LC-MSn confirmed characteristic phytochemical compositions and that increasing % ethanol increased yield of certain components. Milling increased specific ellagitannins, proanthocyanins and triterpenoids from raspberry. CONCLUSIONS: Milling/ oil extraction increased the yield and phytochemical diversity of extracts from raspberry but not from blackcurrant pomace which suggests that the phytochemicals from blackcurrant pomace are largely available on the pomace surfaces.
Pectobacterium atrosepticum is part of a larger family of soft rot bacteria ( Pectobacteriaceae ) that cause disease on a wide range of crops worldwide. They are closely related to members of the Enterobacteriaceae and, as the plant pathogens and plant associated members of the group, form part of a continuum towards opportunistic and more devastating animal and human pathogens. Many of the horizontally acquired islands present in the genome of P. atrosepticum are directly responsible for life on plants. These include genes for a plethora of plant cell wall degrading enzymes, plant toxins, siderophores etc., which are exported by multiple secretion systems under a highly coordinated regulation system.
Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.
It is increasingly apparent that although different genotypes within a species share "core" genes, they also contain variable numbers of "specific" genes and different structures of "core" genes that are only present in a subset of individuals. Using a common reference genome may thus lead to a loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete or misleading transcriptomics analysis results. In this study, we assembled genotype-specific RTD (sRTD) and common reference-based RTD (cRTD) from RNA-seq data of cultivated Barke and Morex barley, respectively. Our quantitative evaluation showed that the sRTD has a significantly higher diversity of transcripts and alternative splicing events, whereas the cRTD missed 40% of transcripts present in the sRTD and it only has ∼70% accurate transcript assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression analysis. However, gene-level quantification is less affected, which may be a reasonable compromise when a high-quality genotype-specific reference is not available.
Neonicotinoid insecticides (NNIs) have been widely used to control insect pests, while their environmental residues and associated hazardous impacts on human and ecosystem health have attracted increasing attention worldwide. In this study, we examined the current levels and associated spatial and temporal patterns of NNIs in multiple environmental media across China. Concentrations of NNIs in surface water, sediment, and soil were in the range of 9.94–755 ng·L⁻¹, 0.07–8.30 ng·g⁻¹ DW, and 0.009–356 ng·g⁻¹ DW, respectively. The high levels of NNIs in surface water, such as in Yangtze River (755 ng·L⁻¹), North River (539 ng·L⁻¹), Nandu River (519 ng·L⁻¹), and Minjiang River (514 ng·L⁻¹), were dominated by imidacloprid, thiamethoxam, and acetamiprid due to their extensive use. The levels of NNIs in sediments were relatively low, and the highest concentration (8.30 ng·g⁻¹ DW) was observed in Dongguan ditch. Sediment–water exchange calculated from fugacity fraction indicated that NNIs in sediment can be released back into the water due to their high solubility and low KOW. Soils from agricultural zones contained the largest residual NNIs, with imidacloprid concentrations in cultivated soil reaching 119 ng·g⁻¹ DW. The calculated leaching potential showed that clothianidin has the highest migration potential to deep soil or groundwater. The monitored data of NNIs presented a decreasing trend from 2016 to 2018, which might be caused by the implementation of relevant control policies for NNI applications. The high levels of NNIs mainly occurred in southern China due to frequent agricultural activities and warm and humid meteorological conditions. The results from this study improve our understanding of the pollution levels and environmental behavior of NNIs in different environmental media across China and provide new knowledge that is needed for making future control policies for NNIs production and application. Graphical abstract
Background Most plants have a hyphosphere, the thin zone of soil around extraradical hyphae of arbuscular mycorrhizal (AM) fungi, which extends beyond the rhizosphere. This important interface has critical roles in plant mineral nutrition and water acquisition, biotic and abiotic stress resistance, mineral weathering, the formation of soil macroaggregates and aggregate stabilization, carbon (C) allocation to soils and interaction with soil microbes. Scope This review focuses on the hyphosphere of AM fungi and critically appraises the important findings related to the hyphosphere processes, including physical, chemical and biological properties and functions. We highlight ecological functions of AM fungal hyphae, which have profound impacts on global sustainability through biological cycling of nutrients, C sequestration in soil, release of greenhouse gas emissions from soil and the diversity and dynamics of the microbial community in the vicinity of the extraradical hyphae. Conclusions As a critical interface between AM fungi and soil, hyphosphere processes and their important ecological functions have begun to be understood and appreciated, and are now known to be implicit in important soil processes. Recent studies provide new insights into this crucial zone and highlight how the hyphosphere might be exploited as a nature-based solution, through understanding of interactions with the microbiome and the impacts on key processes governing resource availability, to increase sustainability of agriculture and minimize its environmental impact. Uncovering hyphosphere chemical and biological processes and their subsequent agricultural, ecological and environmental consequences is a critical research activity.
There are strong links between heritage and the environment yet, heritage is not fully included in existing ecosystem‐based frameworks. Different understandings of heritage values exist, and heritage values are not yet related to key value categories in environmental values research. To address this gap and facilitate a common values‐based approach, we develop a novel framework that links heritage and environmental values. First, we expand the understanding of heritage values by linking heritage to key environmental value categories. We then use the Life Framework of Values to show how heritage features in the different ways in which people relate to the world. The resulting heritage values framework is operationalised by applying it to six case examples drawn from participatory research on the governance of European coastal and maritime heritage. We found that the environment was not only considered to be a setting for heritage but was itself valued as heritage in different ways; that heritage is not extrinsic to the environment but is also a way in which people see meaning in the environment; and that multiple value frames and types were involved in shaping this perspective. The results highlight important discrepancies between stakeholders' perspectives and existing management approaches. Applying the framework shows the ways in which heritage and nature are entwined by providing a structure for elucidating what can be valued as heritage, what values can inform heritage values and how heritage values feature in human–nature relations. Malgré les liens très étroits qui existent entre l’Environnement et le Patrimoine, ce dernier n'est pas pleinement pris en compte dans les cadres de l’analyse écosystémique. Pour le moment, aucun lien n’est établi entre les différentes conceptions existantes de la valeur patrimoniale et les principales catégories retenues par la recherche portant sur les valeurs environnementales. Pour combler cette lacune et faciliter l'adoption d'une approche commune fondée sur les valeurs, nous avons élaboré un nouveau cadre d’analyse alliant valeurs patrimoniales et valeurs environnementales. Pour cela, nous avons enrichi la compréhension des valeurs patrimoniales en reliant le patrimoine aux principales catégories de valeurs environnementales. Puis nous avons utilisé le cadre d’analyse « Life Framework of Values » afin de montrer comment le patrimoine s'inscrit dans le rapport des individus au monde. Le cadre des valeurs patrimoniales qui en résulte a été opérationnalisé en l’appliquant à six exemples issus d’une recherche participative portant sur la gouvernance du patrimoine côtier et maritime européen. Trois principaux éléments peuvent être soulignés: (i) que l'environnement n'est pas uniquement considéré comme un cadre / écrin pour le patrimoine, mais qu'il est lui‐même valorisé en tant que patrimoine; (ii) que le patrimoine n'est pas extrinsèque à l'environnement, mais qu'il est une composante de la manière dont les individus perçoivent l’environnement et lui donnent sens; (iii) et que de multiples modèles et types de valeurs sont impliqués dans la définition de cette approche. Les résultats mettent en évidence des divergences importantes entre les points de vue des parties prenantes et les approches de gestion existantes. L'application de ce cadre d’analyse montre la manière dont le patrimoine et la nature sont liés. Il fournit une structure permettant de déterminer ce qui peut être valorisé en tant que patrimoine; les valeurs pouvant alimenter les valeurs patrimoniales; et de quelles manières les valeurs patrimoniales s’expriment dans les relations homme‐nature. Read the free Plain Language Summary for this article on the Journal blog.
Whether pursuing the breadth of the UN's Sustainable Development Goalsor delivering joined-up approaches within a single environmental domain, it isincreasingly important to understand how policy objectives, policy design andpolicy implementation cohere vertically (within policy) and horizontally(between policies). However, policy coherence remains a challenge to implement.The limited empirical scholarship on policy coherence tends to focus on policydocumentation and/or the outcomes, with little attention to individual agencyor social processes involved. Therefore, our contribution considers theindividuals making policy coherence happen. Furthermore, there is littlediscussion of the normative dimensions of policy coherence making it ripe for apolitical ecology analysis. Empirical research conducted with thoseimplementing policy coherence within four UK catchment (watershed) partnershipsis considered from a critical interpretive policy analysis perspective toenrich the interface between political ecology and environmental policy. We findthat the appetite and ability to support policy coherence depends on individualagency as much as partnership structures. We consider which actors practicepolicy coherence; what motivates those investing their energy into thesecoherence practices; and their constraints. Although it is challenging to researchsuch processes, our data provides insights into the social processes of policycoherence. The explicit political ecology lens highlights how power is involvedin these voluntary initiatives, echoing the critique of traditionalpresentations of integrated water resource management devoid of politics.
Nitrogen‐fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2‐fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen‐fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane‐bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species‐rich pantropical legume clade.
This paper focuses on the use of quantum dots in plant biology as indicators of organic N and inorganic P uptake by, and distribution within, plants, including those with mycorrhizal symbionts. Quantum dots used in this way are fluorescent 2-15 nm diameter CdSe/ZnS semiconductors coated with organic N compounds or with apatite (solid calcium phosphate). While control experiments showed no uptake of the uncoated but otherwise identical quantum dots, experiments by other investigators showed uptake and movement within the plant of some of the other engineered nanoparticles that have been tested. The most likely mechanism of entry of quantum dots is endocytosis, contrasting with the movement of free dissolved amino acids and inorganic phosphate through integral plasma membrane transporters. Further work is needed comparing the results from quantum dot experiments with otherwise identical experiments using ¹⁵N labelling of amino acids and ³²P and/or ³³P labelling of inorganic phosphate not associated with quantum dots to test the validity of this use of quantum dots. A comparison is also needed of the toxicity of CdSe-based quantum dots with that of radioactive P isotopes.
To establish productive infections, viruses must be able both to subdue the host metabolism for their own benefit and to counteract host defences. This frequently results in the establishment of viral–host protein–protein interactions that may have either proviral or antiviral functions. The study of such interactions is essential for understanding the virus–host interplay. Plant viruses with RNA genomes are typically translated, replicated, and encapsidated in the cytoplasm of infected cells. Despite this, a significant array of their encoded proteins has been reported to enter the nucleus, often showing high accumulation at subnuclear structures such as the nucleolus and/or Cajal bodies. However, the biological significance of such a distribution pattern is frequently unknown. Here, we explored whether the nucleolar/Cajal body localization of protein p37 of Pelargonium line pattern virus (PLPV, genus Pelarspovirus, family Tombusviridae), might be related to potential interactions with the nucleolar/Cajal body marker proteins, fibrillarin and coilin. The results revealed that p37, which has a dual role as coat protein and as suppressor of RNA silencing, a major antiviral system in plants, is able to associate with these cellular factors. Analysis of (wildtype and/or mutant) PLPV accumulation in plants with up- or downregulated levels of fibrillarin or coilin have suggested that the former might be involved in an as yet unknown antiviral pathway, which may be targeted by p37. The results suggest that the growing number of functions uncovered for fibrillarin can be wider and may prompt future investigations to unveil the plant antiviral responses in which this key nucleolar component may take part.
Water infrastructures are often living infrastructures, whose operation relies on processes involving other-than-human living beings. This article considers the materiality of waterscapes by attending to this liveliness. We argue that critical water research can benefit from situating social relations and water transformations within more-than-human worlds. Our conceptual framework brings hydrosocial scholarship into conversation with more-than-human geography. This opens avenues for interdisciplinary water research that weaves together ecology and qualitative social research. The analytical potential of such a framework is explored through an empirical account grounded in two constructed wetland projects in rural India. These infrastructural assemblages engage humans, other living beings and objects in webs of material-semiotic processes. We present three stories of intra-action that focus on particular plants, microbes and animals within these waterscapes. Our analysis highlights the crucial importance of other-than-human living beings in the production of waterscape knowledge and suggests a need to go beyond the problematisation of ‘uneven’ waterscapes. Approaching waterscapes as more-than-human collectives prompts us to consider the power relations that underpin waterscape knowledge and the politics of multispecies justice. A focus on more-than-human infrastructures opens up the possibility of interdisciplinary water research that is better attuned to the hybrid nature of social and ecological processes, as well as the politics embedded therein.
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353 members
Richard W Slee
  • Social Economic and Geographical Sciences Group
Sue Jones
  • Information and Computational Science
Euan Kevin James
  • Ecological Sciences Research
Robert D Hancock
  • Cell and Molecular Science
Invergowrie, DD2 5DA, Aberdeen, United Kingdom
Head of institution
Prof. Colin Campbell