Measuring and modelling plant-driven soil carbon dynamics.

Plant root activity and deposition of root carbon (C) into the rhizosphere are known to influence the turnover of existing soil organic matter (SOM) in so- called rhizosphere priming effects (RPE). Thereby soil microbes may access nutrients in SOM which are otherwise unavailable to them. However the magnitudes, drivers and mechanisms of these effects are poorly understood. In this thesis I develop a field system to measure such effects on diurnal, seasonal and longer timescales, and use it to explore RPEs and their drivers in contrasting soils under grass. The field system measures CO₂ fluxes and their ¹³ C isotope composition (δ¹³C) near continuously in large (0.8 m diameter, 1 m deep) lysimeters containing two naturally-structured C₃ soils planted with a C₄ grass. The difference in δ¹³C between C₃ SOM and C₄ plants is used to partition fluxes between plant and soil sources. The system’s accuracy and precision were sufficient to resolve diurnal and seasonal patterns in both plant and soil fluxes. Diurnal changes in plant δ¹³C can cause large partitioning errors. I show how, with long-term datasets with sufficient temporal resolution, part of the dataset can be used to allow for transient shifts in plant and soil δ¹³C. I explored the magnitude and mechanisms of RPEs in the two contrasting soils over two years, and the effect of differences in nitrogen supply. I used solar radiation as a proxy for photosynthesis, root activity and rhizodeposition. I found that seasonal and particularly diurnal patterns in SOM turnover were tightly coupled to solar radiation, and more so than in previously published studies. Model estimates of SOM turnover were improved by the inclusion of solar radiation as an explanatory variable alongside soil moisture and temperature, consistent with RPEs. There was no evidence for differences in RPEs with nitrogen supply in either soil.Otten, Wilfred (Associate) Paterson, Eric (Associate)PhD in Environment and Agrifoo

On allowing for transient variation in end-member δ13C values in partitioning soil C fluxes from net ecosystem respiration

The use of stable isotope analysis to resolve ecosystem respiration into its plant and soil components rests on how well the end-member isotope signatures (δ13C) are characterised. In general, it is assumed that end-member values are constant over time. However, there are necessarily diurnal and other transient variations in end-members with environmental conditions. We analyse diurnal and seasonal patterns of ecosystem respiration and its δ13C in a C4 grass growing in a C3 soil using fixed and diurnally varying plant and soil δ13C end-members. We measure the end-members independently, and we assess the effects of expected variation in values. We show that variation in end-members within realistic ranges, particularly diurnal changes in the plant end-member, can cause partitioning errors of 40% during periods of high plant growth. The effect depends on how close the end-member is to the measured net respiration δ13C, that is, the proportion of the respiration due to that end-member. We show light-driven variation in plant end-members can cause substantial distortion of partitioned soil organic matter (SOM) flux patterns on a diurnal scale and cause underestimation of daily to annual SOM turnover of approximately 25%. We conclude that, while it is not practicable to independently measure the full temporal variation in end-member values over a growing season, this error may be adjusted for by using a diurnally varying δ13Cplant

Contributions and future priorities for soil science: comparing perspectives from scientists and stakeholders

Soils are a fundamental natural resource but intensifying demands and increasing soil degradation necessitate focussed research into the sustainable use of soils. Since soil functioning is critical for the operations and performance of multiple industries, businesses and municipalities, soil scientists need to actively engage with these bodies to orientate research goals towards stakeholder needs. To achieve this, stakeholder views about the current and potential contributions of soil science to different sectors need to be taken into account when setting the future research agenda. Here, we assessed whether the current and future research priorities of soil science match the needs of four major industrial and environmental sectors: agriculture, ecosystem services and natural resources, waste management, and water management. We used an online questionnaire, distributed to 192 organisations and via social media, to compare stakeholders' and scientists' perceptions of (a) the contributions of soil science to date, (b) the areas not currently served by soil science and (c) future research needs in soil science. Stakeholders generally rated the contributions of soil science to date as ‘great’ or ‘fundamental’, but scientists rated the contributions more highly. Respondents identified numerous areas that soil research has not yet sufficiently addressed, which were mostly sector-specific and often overlapped with perceived future research needs. Importantly, stakeholders' and scientists' views of future research priorities differed strongly within sectors, with the notable exception of agriculture, where views were generally consistent. We conclude that soil science may hold unexplored potential in several industrial and environmental sectors. We call for improved research communication and greater stakeholder involvement to shape the future soils research agenda and ensure the sustainable use of soils across multiple areas of society

The three-peat challenge : business as usual, responsible agriculture, and conservation and restoration as management trajectories in global peatlands

FundingThis work was supported by the Natural Environment Research Council [grant numbers NE/X015238/1; NE/ V006444/1; NE/V018760/1], the Royal Geographical Society (RBEA 02.21), the Royal Society (RGS\R2\202229), and Growing Health (BB/X010953/1) BBSRC Institute Strategic Programme.Peer reviewedPublisher PD

Adenosine closes the K+ channel KCa3.1 in human lung mast cells and inhibits their migration via the adenosine A2A receptor

Human lung mast cells (HLMC) express the Ca2+-activated K+ channel KCa3.1, which opens following IgE-dependent activation. This hyperpolarises the cell membrane and potentiates both Ca2+ influx and degranulation. In addition, blockade of KCa3.1 profoundly inhibits HLMC migration to a variety of diverse chemotactic stimuli. KCa3.1 activation is attenuated by the β2adrenoceptor through a Gαs-coupled mechanism independent of cyclic AMP. Adenosine is an important mediator that both attenuates and enhances HLMC mediator release through the Gαs-coupled A2A and A2B adenosine receptors, respectively. We show that at concentrations that inhibit HLMC degranulation (10–5–10–3 M), adenosine closes KCa3.1 both dose-dependently and reversibly. KCa3.1 suppression by adenosine was reversed partially by the selective adenosine A2A receptor antagonist ZM241385 but not by the A2B receptor antagonist MRS1754, and the effects of adenosine were mimicked by the selective A2A receptor agonist CGS21680. Adenosine also opened a depolarising current carried by non-selective cations. As predicted from the role of KCa3.1 in HLMC migration, adenosine abolished HLMC chemotaxis to asthmatic airway smooth muscle-conditioned medium. In summary, the Gαs-coupled adenosine A2A receptor closes KCa3.1, providing a clearly defined mechanism by which adenosine inhibits HLMC migration and degranulation. A2A receptor agonists with channel-modulating function may be useful for the treatment of mast cell-mediated disease

The Stakes in Bayh-Dole: Public Values Beyond the Pace of Innovation

Evaluation studies of the Bayh-Dole Act are generally concerned with the pace of innovation or the transgressions to the independence of research. While these concerns are important, I propose here to expand the range of public values considered in assessing Bayh-Dole and formulating future reforms. To this end, I first examine the changes in the terms of the Bayh-Dole debate and the drift in its design. Neoliberal ideas have had a definitive influence on U.S. innovation policy for the last thirty years, including legislation to strengthen patent protection. Moreover, the neoliberal policy agenda is articulated and justified in the interest of “competitiveness.” Rhetorically, this agenda equates competitiveness with economic growth and this with the public interest. Against that backdrop, I use Public Value Failure criteria to show that values such as political equality, transparency, and fairness in the distribution of the benefits of innovation, are worth considering to counter the “policy drift” of Bayh-Dole

On pedagogy of a Soil Science Centre for Doctoral Training

Here we describe and evaluate the success of a multi-institutional Centre for Doctoral Training (CDT), which was established to address a UK skills shortage in Soil Science. The government-funded ‘STARS’ (Soils Training And Research Studentships) CDT was established in 2015 across a range of universities and research institutes in the UK. It recruited 41 PhD students equitably split across the institutions under four core research themes identified as being central to the national need, namely, (1) Understanding the soil–root interface, (2) Soils and the delivery of ecosystem services, (3) Resilience and response of functions in soil systems and (4) Modelling the soil ecosystem at different spatial and temporal scales. In addition, the STARS CDT provided a diverse skills programme, including: Holistic training in soils, the promotion of collegiality and joint working, strategies to promote science and generate impact, internships with end users (e.g., policymakers, industry), personal wellbeing, and ways to generate a lasting soils training legacy. Overall, both supervisors and students have reported a positive experience of the CDT in comparison to the conventional doctoral training programmes, which have less discipline focus and little chance for students to scientifically interact with their cohorts or to undertake joint training activities. The STARS CDT also allowed students to freely access research infrastructure across the partner institutions (e.g., long-term field trials, specialised analytical facilities, high-performance computing), breaking down traditional institutional barriers and thus maximising the students' potential to undertake high-quality research. The success and legacy of the STARS CDT can be evidenced in many ways; however, it is exemplified by the large number and diversity of journal papers produced, the lasting collaborations, final career destinations, and creation of a web-based legacy portal including new and reflective video material.STARS CDT, Grant/Award Numbers: NE/V017667/1, NE/R010218/1, NE/M009106/1; UKR

Characterizing Strain Variation in Engineered<i> E. coli</i> Using a Multi-Omics-Based Workflow

Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology, provides molecular insight into how the host organism microenvironment changes due to pathway engineering, and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof-of-concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks

Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

AbstractThe identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery.</jats:p