Peatland hydrology and carbon release: why small-scale process matters

Peatlands cover over 400 million hectares of the Earth's surface and store between one-third and one-half of the world's soil carbon pool. The long-term ability of peatlands to absorb carbon dioxide from the atmosphere means that they play a major role in moderating global climate. Peatlands can also either attenuate or accentuate flooding. Changing climate or management can alter peatland hydrological processes and pathways for water movement across and below the peat surface. It is the movement of water in peats that drives carbon storage and flux. These small-scale processes can have global impacts through exacerbated terrestrial carbon release. This paper will describe advances in understanding environmental processes operating in peatlands. Recent (and future) advances in high-resolution topographic data collection and hydrological modelling provide an insight into the spatial impacts of land management and climate change in peatlands. Nevertheless, there are still some major challenges for future research. These include the problem that impacts of disturbance in peat can be irreversible, at least on human time-scales. This has implications for the perceived success and understanding of peatland restoration strategies. In some circumstances, peatland restoration may lead to exacerbated carbon loss. This will also be important if we decide to start to create peatlands in order to counter the threat from enhanced atmospheric carbon

Water footprinting of pasture-based farms; beef and sheep

peer-reviewedIn the context of water use for agricultural production, water footprints (WFs) have become an important sustainability indicator. To understand better the water demand for beef and sheep meat produced on pasture-based systems, a WF of individual farms is required. The main objective of this study was to determine the primary contributors to freshwater consumption up to the farm gate expressed as a volumetric WF and associated impacts for the production of 1 kg of beef and 1 kg of sheep meat from a selection of pasture-based farms for 2 consecutive years, 2014 and 2015. The WF included green water, from the consumption of soil moisture due to evapotranspiration, and blue water, from the consumption of ground and surface waters. The impact of freshwater consumption on global water stress from the production of beef and sheep meat in Ireland was also computed. The average WF of the beef farms was 8391 l/kg carcass weight (CW) of which 8222 l/kg CW was green water and 169 l/kg CW was blue water; water for the production of pasture (including silage and grass) contributed 88% to the WF, concentrate production – 10% and on-farm water use – 1%. The average stress-weighted WF of beef was 91 l H2O eq/kg CW, implying that each kg of beef produced in Ireland contributed to freshwater scarcity equivalent to the consumption of 91 l of freshwater by an average world citizen. The average WF of the sheep farms was 7672 l/kg CW of which 7635 l/kg CW was green water and 37 l/kg CW was blue water; water for the production of pasture contributed 87% to the WF, concentrate production – 12% and on-farm water use – 1%. The average stress-weighted WF was 2 l H2O eq/kg CW for sheep. This study also evaluated the sustainability of recent intensification initiatives in Ireland and found that increases in productivity were supported through an increase in green water use and higher grass yields per hectare on both beef and sheep farms

The Double Spade Method: a ‘mini-profile’ visual soil evaluation technique

peer-reviewedVisual Soil Evaluation (VSE) methods are established for soil quality assessment and focus on the examination of soil structure and associated anthropogenic impacts. VSE techniques, of which numerous types exist, are successfully used internationally both in soil research and as sustainable soil management tools. Techniques are generally categorised into profile and spade methods. Profile methods examine entire soil profiles in soil-pits to depths of ~ 1.5 m, exploring interactions between inherent soil features and anthropic management at specific sample points. Spade methods examine the upper soil profile, often by extracting sample blocks of topsoil by spade and focus on anthropic impacts. The VESS method (Guimarães et al., 2011) is a widely used spade method and involves assessment of soil sample blocks to 25 cm depth. However, in arable soils, important structural features may occur just below this depth such as plough pans, which VESS may not capture. The SubVESS method (Ball et al., 2015) follows principles of VESS but allows assessment to ~ 1 m depth. However, the later involves soil-pit excavation by mechanical means, which may be destructive, costly, time consuming and limit replication. When used in on-farm situations by farmers or advisors, full soil-pit excavation may not be desirable. Here we describe a method previously outlined (Emmet-Booth et al. 2018) called the Double Spade Method (DS) designed to examine miniprofiles in soil pits to 40 cm depth, therefore capturing potential structural features below the VESS assessment depth, without requiring full soil-pit excavation

Exploring the sensitivity of visual soil evaluation to traffic-induced soil compaction

peer-reviewedVisual Soil Evaluation (VSE) techniques are useful for assessing the impact of land management, particularly the identification and remediation of soil compaction. Despite an increasing body of VSE research, comparatively few studies have explored the sensitivity of VSE for capturing experimentally imposed compaction to estimate sensitivity and limit of detection. The aim of this research was to examine the ability of VSE techniques to indicate soil structure at different soil profile depths and to measure the associated soil productive function (yield) response to imposed compaction. A two-year experiment was conducted on sites with loam and sandy soils. Varying levels of wheeled traffic were imposed on plots in a randomised block design, prior to sowing winter barley (Hordeum vulgare L.). Quantitative crop and soil measurements were taken throughout the season in conjunction with VSE techniques, which assessed to 25 cm (VESS), 40 cm (Double Spade) and 80 cm (SubVESS) depth. Graduated changes were observed by soil and some crop quantitative measurements as traffic treatment varied. VESS and Double Spade successfully identified a graduated treatment effect at all sites to 40 cm depth, although diagnosis translated into a yield response for the loam but not the sandy soil. Correlation between VESS Sq scores and crop yield were found. SubVESS gave mixed signals and indicated impacts lower in the profile in certain instances. These impacts were not captured by quantitative soil measurements. This work highlights the capacity for VSE techniques to indicate soil structural damage, which may cause a crop yield response, therefore allowing appropriate soil management strategies to be deployed before yield penalties occur

Scenario analysis report with policy recommendations: An assessment of sustainability, resilience, efficiency and fairness and effective chain relationships in VALUMICS case studies : Deliverable 8.4

This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/. The final version of this report is available at https://doi.org/10.5281/zenodo.6534011The functioning of food value chains entails a complex organisation from farm to fork which is characterised by various governance forms and externalities which have shaped the overall food system. VALUMICS food value chain case studies: wheat to bread, dairy cows to milk, beef cattle to steak, farmed salmon to fillets and tomato to processed tomato were selected to enable explorative and empirical analysis to better understand the functioning of the food system and, to identify the main challenges that need to be addressed to improve sustainability, integrity, resilience, and fairness of European food chains. The VALUMICS system analysis was executed through four operational phases starting with Groundwork & analysis including mapping specific attributes and impacts of food value chains and their externalities. This was followed by Case study baseline analysis, which provided input to the third phase on Modelling and exploration of future scenarios and finally Policy and synthesis of the overall work. This report is an overall synthesis of the VALUMICS results as follows: • Key findings from the VALUMICS project on the functioning of European food value chains and their impacts on more sustainable, resilient, fairer, and transparent food system are summarised through a compilation of 25 Research Findings and Policy Briefs. • By highlighting the major contributions from the research activities throughout the four phases of the VALUMICS project, this report delivers an assessment of various factors influencing sustainability, resilience, efficiency and fairness and effective chain relationships of different food value chains, and their determinants. • The synthesis of the outcome allows the identification of opportunities and challenges characterising the functioning of food supply chains, and thus, the prospects and potentials for strengthening the EU food sector

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript

Accelarated immune ageing is associated with COVID-19 disease severity

Background The striking increase in COVID-19 severity in older adults provides a clear example of immunesenescence, the age-related remodelling of the immune system. To better characterise the association between convalescent immunesenescence and acute disease severity, we determined the immune phenotype of COVID-19 survivors and non-infected controls. Results We performed detailed immune phenotyping of peripheral blood mononuclear cells isolated from 103 COVID-19 survivors 3–5 months post recovery who were classified as having had severe (n = 56; age 53.12 ± 11.30 years), moderate (n = 32; age 52.28 ± 11.43 years) or mild (n = 15; age 49.67 ± 7.30 years) disease and compared with age and sex-matched healthy adults (n = 59; age 50.49 ± 10.68 years). We assessed a broad range of immune cell phenotypes to generate a composite score, IMM-AGE, to determine the degree of immune senescence. We found increased immunesenescence features in severe COVID-19 survivors compared to controls including: a reduced frequency and number of naïve CD4 and CD8 T cells (p < 0.0001); increased frequency of EMRA CD4 (p < 0.003) and CD8 T cells (p < 0.001); a higher frequency (p < 0.0001) and absolute numbers (p < 0.001) of CD28−ve CD57+ve senescent CD4 and CD8 T cells; higher frequency (p < 0.003) and absolute numbers (p < 0.02) of PD-1 expressing exhausted CD8 T cells; a two-fold increase in Th17 polarisation (p < 0.0001); higher frequency of memory B cells (p < 0.001) and increased frequency (p < 0.0001) and numbers (p < 0.001) of CD57+ve senescent NK cells. As a result, the IMM-AGE score was significantly higher in severe COVID-19 survivors than in controls (p < 0.001). Few differences were seen for those with moderate disease and none for mild disease. Regression analysis revealed the only pre-existing variable influencing the IMM-AGE score was South Asian ethnicity ( = 0.174, p = 0.043), with a major influence being disease severity ( = 0.188, p = 0.01). Conclusions Our analyses reveal a state of enhanced immune ageing in survivors of severe COVID-19 and suggest this could be related to SARS-Cov-2 infection. Our data support the rationale for trials of anti-immune ageing interventions for improving clinical outcomes in these patients with severe disease