Trade-offs constrain the success of glyphosate-free farming.

Glyphosate, the most widely used herbicide, is linked with environmental harm and there is a drive to replace it in agricultural systems. We model the impacts of discontinuing glyphosate use and replacing it with cultural control methods. We simulate winter wheat arable systems reliant on glyphosate and typical in northwest Europe. Removing glyphosate was projected to increase weed abundance, herbicide risk to the environment, and arable plant diversity and decrease food production. Weed communities with evolved resistance to non-glyphosate herbicides were not projected to be disproportionately affected by removing glyphosate, despite the lack of alternative herbicidal control options. Crop rotations with more spring cereals or grass leys for weed control increased arable plant diversity. Stale seedbed techniques such as delayed drilling and choosing ploughing instead of minimum tillage had varying effects on weed abundance, food production, and profitability. Ploughing was the most effective alternative to glyphosate for long-term weed control while maintaining production and profit. Our findings emphasize the need for careful consideration of trade-offs arising in scenarios where glyphosate is removed. Integrated Weed Management (IWM) with more use of cultural control methods offers the potential to reduce chemical use but is sensitive to seasonal variability and can incur negative environmental and economic impacts.

Evidence for functional state transitions in intensively-managed soil ecosystems.

Soils are fundamental to terrestrial ecosystem functioning and food security, thus their resilience to disturbances is critical. Furthermore, they provide effective models of complex natural systems to explore resilience concepts over experimentally-tractable short timescales. We studied soils derived from experimental plots with different land-use histories of long-term grass, arable and fallow to determine whether regimes of extreme drying and re-wetting would tip the systems into alternative stable states, contingent on their historical management. Prior to disturbance, grass and arable soils produced similar respiration responses when processing an introduced complex carbon substrate. A distinct respiration response from fallow soil here indicated a different prior functional state. Initial dry:wet disturbances reduced the respiration in all soils, suggesting that the microbial community was perturbed such that its function was impaired. After 12 drying and rewetting cycles, despite the extreme disturbance regime, soil from the grass plots, and those that had recently been grass, adapted and returned to their prior functional state. Arable soils were less resilient and shifted towards a functional state more similar to that of the fallow soil. Hence repeated stresses can apparently induce persistent shifts in functional states in soils, which are influenced by management history.

Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community.

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.

The North Wyke Farm Platform: effect of temperate grassland farming systems on soil moisture contents, runoff and associated water quality dynamics.

The North Wyke Farm Platform was established as a United Kingdom national capability for collaborative research, training and knowledge exchange in agro-environmental sciences. Its remit is to research agricultural productivity and ecosystem responses to different management practices for beef and sheep production in lowland grasslands. A system based on permanent pasture was implemented on three 21-ha farmlets to obtain baseline data on hydrology, nutrient cycling and productivity for 2 years. Since then two farmlets have been modified by either (i) planned reseeding with grasses that have been bred for enhanced sugar content or deep-rooting traits or (ii) sowing grass and legume mixtures to reduce nitrogen fertilizer inputs. The quantities of nutrients that enter, cycle within and leave the farmlets were evaluated with data recorded from sensor technologies coupled with more traditional field study methods. We demonstrate the potential of the farm platform approach with a case study in which we investigate the effects of the weather, field topography and farm management activity on surface runoff and associated pollutant or nutrient loss from soil. We have the opportunity to do a full nutrient cycling analysis, taking account of nutrient transformations in soil, and flows to water and losses to air. The NWFP monitoring system is unique in both scale and scope for a managed land-based capability that brings together several technologies that allow the effect of temperate grassland farming systems on soil moisture levels, runoff and associated water quality dynamics to be studied in detail. HIGHLIGHTS: Can meat production systems be developed that are productive yet minimize losses to the environment?The data are from an intensively instrumented capability, which is globally unique and topical.We use sensing technologies and surveys to show the effect of pasture renewal on nutrient losses.Platforms provide evidence of the effect of meteorology, topography and farm activity on nutrient loss.

On the origin of carbon dioxide released from rewetted soils.

When dry soils are rewetted a pulse of CO2 is invariably released, and whilst this phenomenon has been studied for decades, the precise origins of this CO2 remain obscure. We postulate that it could be of chemical (i.e. via abiotic pathways), biochemical (via free enzymes) or biological (via intact cells) origin. To elucidate the relative contributions of the pathways, dry soils were either sterilised (double autoclaving) or treated with solutions of inhibitors (15% trichloroacetic acid or 1% silver nitrate) targeting the different modes. The rapidity of CO2 release from the soils after the drying:rewetting (DRW) cycle was remarkable, with maximal rates of evolution within 6 min, and 41% of the total efflux over 96 h released within the first 24 h. The complete cessation of CO2 eflux following sterilisation showed there was no abiotic (dissolution of carbonates) contribution to the CO2 release on rewetting, and clear evidence for an organismal or biochemical basis to the flush. Rehydration in the presence of inhibitors indicated that there were approximately equal contributions from biochemical (outside membranes) and organismal (inside membranes) sources within the first 24 h after rewetting. This suggests that some of the flux was derived from microbial respiration, whilst the remainder was a consequence of enzyme activity, possibly through remnant respiratory pathways in the debris of dead cells.

Long-term management changes topsoil and subsoil organic carbon and nitrogen dynamics in a temperate agricultural system.

Soil organic carbon (SOC) and nitrogen (N) contents are controlled partly by plant inputs that can be manipulated in agricultural systems. Although SOC and N pools occur mainly in the topsoil (upper 0.30 m), there are often substantial pools in the subsoil that are commonly assumed to be stable. We tested the hypothesis that contrasting long-term management systems change the dynamics of SOC and N in the topsoil and subsoil (to 0.75 m) under temperate conditions. We used an established field experiment in the UK where control grassland was changed to arable (59 years before) and bare fallow (49 years before) systems. Losses of SOC and N were 65 and 61% under arable and 78 and 74% under fallow, respectively, in the upper 0.15 m when compared with the grass land soil, whereas at 0.3-0.6-m depth losses under arable and fallow were 41 and 22% and 52 and 35%, respectively. The stable isotopes 13C and 15N showed the effects of different treatments. Concentrations of long-chain n-alkanes C27, C29 and C31 were greater in soil under grass than under arable and fallow. The dynamics of SOC and N changed in both topsoil and subsoil on a decadal time-scale because of changes in the balance between inputs and turnover in perennial and annual systems. Isotopic and geochemical analyses suggested that fresh inputs and decomposition processes occur in the subsoil. There is a need to monitor and predict long-term changes in soil properties in the whole soil profile if soil is to be managed sustainably. HIGHLIGHTS: Land-use change affects soil organic carbon and nitrogen, but usually the topsoil only is considered.Grassland cultivated to arable and fallow lost 13-78% SOC and N to 0.6 m depth within decades.Isotopic and biomarker analyses suggested changes in delivery and turnover of plant-derived inputs.The full soil profile must be considered to assess soil quality and sustainability.

Defining and quantifying the resilience of responses to disturbance: a conceptual and modelling approach from soil science.

There are several conceptual definitions of resilience pertaining to environmental systems and, even if resilience is clearly defined in a particular context, it is challenging to quantify. We identify four characteristics of the response of a system function to disturbance that relate to "resilience": (1) degree of return of the function to a reference level; (2) time taken to reach a new quasi-stable state; (3) rate (i.e. gradient) at which the function reaches the new state; (4) cumulative magnitude of the function (i.e. area under the curve) before a new state is reached. We develop metrics to quantify these characteristics based on an analogy with a mechanical spring and damper system. Using the example of the response of a soil function (respiration) to disturbance, we demonstrate that these metrics effectively discriminate key features of the dynamic response. Although any one of these characteristics could define resilience, each may lead to different insights and conclusions. The salient properties of a resilient response must thus be identified for different contexts. Because the temporal resolution of data affects the accurate determination of these metrics, we recommend that at least twelve measurements are made over the temporal range for which the response is expected.

150years of macronutrient change in unfertilized UK ecosystems: Observations vs simulations.

Understanding changes in plant-soil C, N and P using data alone is difficult due to the linkages between carbon, nitrogen and phosphorus cycles (C, N and P), and multiple changing long-term drivers (e.g. climate, land-use, and atmospheric N deposition). Hence, dynamic models are a vital tool for disentangling these drivers, helping us understand the dominant processes and drivers and predict future change. However, it is essential that models are tested against data if their outputs are to be concluded upon with confidence. Here, a simulation of C, N and P cycles using the N14CP model was compared with time-series observations of C, N and P in soils and biomass from the Rothamsted Research long-term experiments spanning 150years, providing an unprecedented temporal integrated test of such a model. N14CP reproduced broad trends in soil organic matter (SOM) C, N and P, vegetation biomass and N and P leaching. Subsequently, the model was used to decouple the effects of land management and elevated nitrogen deposition in these experiments. Elevated N deposition over the last 150years is shown to have increased net primary productivity (NPP) 4.5-fold and total carbon sequestration 5-fold at the Geescroft Wilderness experiment, which was re-wilded to woodland in 1886. In contrast, the model predicts that for cropped grassland conditions at the Park Grass site, elevated N deposition has very little effect on SOM, as increases in NPP are diverted from the soil. More broadly, these results suggest that N deposition is likely to have had a large effect on SOM and NPP in northern temperate and boreal semi-natural grasslands and forests. However, in cropped and grazed systems in the same region, whilst NPP may have been supported in part by elevated N deposition, declines in SOM may not have been appreciably counteracted by increased N availability.

Simulation of nitrous oxide emissions at field scale using the SPACSYS model.

Nitrous oxide emitted to the atmosphere via the soil processes of nitrification and denitrification plays an important role in the greenhouse gas balance of the atmosphere and is involved in the destruction of stratospheric ozone. These processes are controlled by biological, physical and chemical factors such as growth and activity of microbes, nitrogen availability, soil temperature and water availability. A comprehensive understanding of these processes embodied in an appropriate model can help develop agricultural mitigation strategies to reduce greenhouse gas emissions, and help with estimating emissions at landscape and regional scales. A detailed module to describe the denitrification and nitrification processes and nitrogenous gas emissions was incorporated into the SPACSYS model to replace an earlier module that used a simplified first-order equation to estimate denitrification and was unable to distinguish the emissions of individual nitrogenous gases. A dataset derived from a Scottish grassland experiment in silage production was used to validate soil moisture in the top 10 cm soil, cut biomass, nitrogen offtake and N2O emissions. The comparison between the simulated and observed data suggested that the new module can provide a good representation of these processes and improve prediction of N2O emissions. The model provides an opportunity to estimate gaseous N emissions under a wide range of management scenarios in agriculture, and synthesises our understanding of the interaction and regulation of the processes.

A review of the impacts of degradation threats on soil properties in the UK.

National governments are becoming increasingly aware of the importance of their soil resources and are shaping strategies accordingly. Implicit in any such strategy is that degradation threats and their potential effect on important soil properties and functions are defined and understood. In this paper, we aimed to review the principal degradation threats on important soil properties in the UK, seeking quantitative data where possible. Soil erosion results in the removal of important topsoil and, with it, nutrients, C and porosity. A decline in soil organic matter principally affects soil biological and microbiological properties, but also impacts on soil physical properties because of the link with soil structure. Soil contamination affects soil chemical properties, affecting nutrient availability and degrading microbial properties, whilst soil compaction degrades the soil pore network. Soil sealing removes the link between the soil and most of the 'spheres', significantly affecting hydrological and microbial functions, and soils on re-developed brownfield sites are typically degraded in most soil properties. Having synthesized the literature on the impact on soil properties, we discuss potential subsequent impacts on the important soil functions, including food and fibre production, storage of water and C, support for biodiversity, and protection of cultural and archaeological heritage. Looking forward, we suggest a twin approach of field-based monitoring supported by controlled laboratory experimentation to improve our mechanistic understanding of soils. This would enable us to better predict future impacts of degradation processes, including climate change, on soil properties and functions so that we may manage soil resources sustainably.

An alphavirus replicon-derived candidate vaccine against Rift Valley fever virus.

Rift Valley fever virus (RVFV) is a mosquito-transmitted bunyavirus (genus Phlebovirus) associated with severe disease in livestock and fatal encephalitis or haemorrhagic fever in a proportion of infected humans. Although live attenuated and inactivated vaccines have been used in livestock, and on a limited scale in humans, there is a need for improved anti-RVFV vaccines. Towards this goal, Sindbis virus replicon vectors expressing the RVFV Gn and Gc glycoproteins, as well as the non-structural nsM protein, were constructed and evaluated for their ability to induce protective immune responses against RVFV. These replicon vectors were shown to produce the RVFV glycoproteins to high levels in vitro and to induce systemic anti-RVFV antibody responses in immunized mice, as determined by RVFV-specific ELISA, fluorescent antibody tests, and demonstration of a neutralizing antibody response. Replicon vaccination also provided 100% protection against lethal RVFV challenge by either the intraperitoneal or intranasal route. Furthermore, preliminary results indicate that the replicon vectors elicit RVFV-specific neutralizing antibody responses in vaccinated sheep. These results suggest that alphavirus-based replicon vectors can induce protective immunity against RVFV, and that this approach merits further investigation into its potential utility as a RVFV vaccine.

Effects of rapid antigen degradation and VEE glycoprotein specificity on immune responses induced by a VEE replicon vaccine.

Genetic vaccines are engineered to produce immunogens de novo in the cells of the host for stimulation of a protective immune response. In some of these systems, antigens engineered for rapid degradation have produced an enhanced cellular immune response by more efficient entry into pathways for processing and presentation of MHC class I peptides. VEE replicon particles (VRP), single cycle vaccine vectors derived from Venezuelan equine encephalitis virus (VEE), are examined here for the effect of an increased rate of immunogen degradation on VRP vaccine efficacy. VRP expressing the matrix capsid (MA/CA) portion of SIV Gag were altered to promote rapid degradation of MA/CA by various linkages to co-translated ubiquitin or by destabilizing mutations and were used to immunize BALB/c mice for quantitation of anti-MA/CA cellular and humoral immune responses. Rapid degradation by the N-end rule correlated with a dampened immune response relative to unmodified MA/CA when the VRP carried a glycoprotein spike from an attenuated strain of VEE. In contrast, statistically equivalent numbers of IFNgamma(+)T-cells resulted when VRP expressing unstable MA/CA were packaged with the wild-type VEE glycoproteins. These results suggest that the cell types targeted in vivo by VRP carrying mutant or wild type glycoprotein spikes are functionally different, and are consistent with previous findings suggesting that wild-type VEE glycoproteins preferentially target professional antigen presenting cells that use peptides generated from the degraded antigen for direct presentation on MHC.

Carbon sequestration in European soils through straw incorporation: limitations and alternatives.

We compared alternate uses of cereal straw (4.25t dry matter ha(-1) containing 1.7t carbon (C)) for their effectiveness in relation to climate change mitigation. The scenarios were (1) incorporation into soil to increase soil organic carbon (SOC) content ("carbon sequestration") and (2) combustion to generate electricity. The Rothamsted Carbon Model was used to estimate SOC accumulation in a silty clay loam soil under the climatic conditions of north-west Europe. Using straw for electricity generation saved seven times more CO2 than from SOC accumulation. This comparison assumed that electricity from straw combustion displaced that generated from coal and used the mean annual accumulation of SOC over 100yr. SOC increased most rapidly in the early years, but then more slowly as a new equilibrium value was approached. We suggest that increased SOC from straw incorporation does not represent genuine climate change mitigation through carbon sequestration. In Europe, most straw not already incorporated in the field where it is grown is subsequently returned elsewhere, e.g., after use for animal bedding and production of manure. Only additional retention of C in soil compared to the alternative use represents sequestration. Maintenance of SOC for soil functioning is a more appropriate rationale for returning straw to soil than climate change mitigation. This analysis shows that considerably greater climate change mitigation is achieved through saved CO2 emissions by burning straw for electricity generation, replacing some use of fossil fuel.

Asymmetric segregation of Numb in retinal development and the influence of the pigmented epithelium.

Asymmetric segregation of cell-fate determinants during cytokinesis plays an important part in controlling cell-fate choice in invertebrates. During Drosophila neurogenesis, for example, asymmetric segregation of the Numb protein, which inhibits Notch signaling, is necessary for the two daughter cells of a division to have different fates. In vertebrates, the role of asymmetric segregation of cell-fate determinants is uncertain, and the way the process might be regulated is unknown. We have studied the orientation of cell divisions and the distribution of Numb in the developing rat retina. We show that, whereas most retinal neuroepithelial cells divide with their mitotic spindles oriented parallel to the plane of the neuroepithelium, a substantial minority divides with their spindles oriented perpendicularly. The proportion of these vertically dividing cells changes during development, peaking around the day of birth. Numb appears to be inherited only by the apical daughter cell when a neuroepithelial cell divides vertically. Similarly, in dissociated cell cultures, some retinal neuroepithelial cells divide asymmetrically and distribute Numb to only one of the two daughter cells, suggesting that the dissociated cells can retain their polarity in vitro. Using retinal explant cultures, we find that the retinal pigment epithelium apparently promotes vertical divisions in the neural retina. To our knowledge, this is the first evidence that asymmetric segregation of cell-fate determinants may contribute to cell diversification in the mammalian retina and that an epithelium controls this process by influencing the plane of division in the adjacent neural retina.

Phenotype of B cells responding to the thymus-independent type-2 antigen polyvinyl pyrrolidinone.

We have determined the origin and cell surface phenotype of B cells producing antibody in response to immunization with the non-self TI-2 antigen polyvinyl pyrrolidinone (PVP). We report that the responding cells are derived from precursors in adult bone marrow and display the phenotype characteristic of B-1 cells. By use of allotype marked chimeric mice, constructed by reconstituting lethally irradiated recipients with adult bone marrow and peritoneal B-1 lymphocytes of recognizably different Ig allotypes, immunized with 1 microgram PVP, we found that although a substantial part of the total IgM produced in these chimeras bore the allotype of the transferred peritoneal B-1 cells, essentially all of the anti-PVP IgM expressed the allotype of the adult bone marrow. Fifteen of 16 hybridomas derived from a normal PVP-immune adult mouse bore N nucleotides at the V-D and D-J junctions of their heavy chain CDR3 regions, indicating their origin from precursors in the adult bone marrow. By use of ELISA spot analysis, we found the cells responding to PVP to be localized in the spleens of normal immunized mice. We then used multiparameter flow cytometric sorting to determine the cell surface phenotype of these cells. We found that the cells producing anti-PVP were greatly enriched in a small subpopulation with the phenotypic characteristics of B-1 cells; they were B220intermediate, CD5low, IgMhigh, IgDlow, CD43+ and CD23-. This subpopulation was also enriched for all cells producing IgM, regardless of specificity (the so-called 'spontaneous' antibody). We conclude that the B-1 phenotype is more likely a marker for a state of differentiation than for a discrete lineage of B cells.

Differences in the temporal properties of human longwave- and middlewave-sensitive cones.

In recent years a number of electrophysiological and psychophysical observations have suggested that the temporal properties of the human longwave- and middlewave-sensitive cones might be different. However, until now the issue has remained unresolved, despite its obvious importance. We have succeeded in probing, electrophysiologically, the temporal properties of the two classes, under a range of adapting conditions, in a normal human observer. Here we present evidence that the temporal properties of these cone types are indeed different and that this difference is constant irrespective of the state of light adaptation, suggesting that light adaptation has little effect on the kinetics of transduction in human cones.

Melanin and the regulation of mammalian photoreceptor topography.

Melanin, or products directly associated with it, regulates the maturation of the neural retina because in hypopigmented mammals the central retina fails to develop fully. To determine whether this deficit is reflected in the distribution of photoreceptors, their topography has been studied in the retinae of normally reared pigmented and albino ferrets and animals reared under reduced light conditions. In both strains, the general distribution of rods and cones was similar to that in the cat, cone density peaking in the central retina and rod density peaking in an annulus around the area centralis. The cone population was organized in the form of an orderly mosaic whose regularity was measured at a wide range of retinal eccentricities. No differences were found in cone numbers or their mosaic distribution between pigmented and albino strains, either at the area centralis or at more peripheral regions. In both cases order within the cone mosaic was independent of density or retinal eccentricity. In the albinos there was a significant deficit in the number of rods at all retinal locations when compared with rod numbers in the pigmented animals. There were no differences between normally reared and dark-reared animals in this respect either within or between the strains. Therefore, the albino gene must have a selective and specific effect on the development of this cell type in the outer retina. Ganglion cells and rods are both affected by the albino gene, while cones are not. Because cones and ganglion cells are generated during the same period and rods are generated later, the albino gene cannot be acting during a particular developmental time window. Because the cone mosaic was normal in the albinos, in spite of a large rod deficit, the factors that regulate the spacing of cones cannot depend in any significant manner upon the later generation and subsequent addition of rods to the outer retina.

Visual pigments and oil droplets in genetically manipulated and carotenoid deprived quail: a microspectrophotometric study.

The spectral absorbances of visual pigments and retinal oil droplets were studied in three groups of Japanese quail (Coturnix coturnix japonica): an unselected control population and two artificially selected strains that exhibited different early approach preferences between blue and red stimuli. The oil droplets were examined with and without prior carotenoid deprivation. Four cone pigments and five oil droplet types were identified, resembling those in other avian species. Carotenoid deprivation eliminated all pigmentation detectable in oil droplets by microspectrophotometry. Placement of chicks on normal diet gradually reintroduced normal pigmentation within the span of about a week. No statistically significant differences were found between normal and genetically selected birds in either visual pigments or oil droplet types, or in their relative proportions. It is concluded that differences in the early colour preferences of quail are unlikely to be a result of variation in the spectral properties of their photoreceptors.