Global change pressures on soils from land use and management.

Soils are subject to varying degrees of direct or indirect human disturbance, constituting a major global change driver. Factoring out natural from direct and indirect human influence is not always straightforward, but some human activities have clear impacts. These include land-use change, land management and land degradation (erosion, compaction, sealing and salinization). The intensity of land use also exerts a great impact on soils, and soils are also subject to indirect impacts arising from human activity, such as acid deposition (sulphur and nitrogen) and heavy metal pollution. In this critical review, we report the state-of-the-art understanding of these global change pressures on soils, identify knowledge gaps and research challenges and highlight actions and policies to minimize adverse environmental impacts arising from these global change drivers. Soils are central to considerations of what constitutes sustainable intensification. Therefore, ensuring that vulnerable and high environmental value soils are considered when protecting important habitats and ecosystems, will help to reduce the pressure on land from global change drivers. To ensure that soils are protected as part of wider environmental efforts, a global soil resilience programme should be considered, to monitor, recover or sustain soil fertility and function, and to enhance the ecosystem services provided by soils. Soils cannot, and should not, be considered in isolation of the ecosystems that they underpin and vice versa. The role of soils in supporting ecosystems and natural capital needs greater recognition. The lasting legacy of the International Year of Soils in 2015 should be to put soils at the centre of policy supporting environmental protection and sustainable development.

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems.

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant-soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.

Spatial properties affecting the sensitivity of soil water dissolved organic carbon long-term median concentrations and trends.

It is increasingly clear that increases in dissolved organic carbon in upland waters in recent decades have often been dominated by acid deposition, but reasons for substantial variation in rates of change remain unclear. This paper focuses on the extent to which spatial properties, such as variation in soil properties, atmospheric deposition and climate, affect the sensitivity of DOC concentrations in soil water. The purpose is to i) examine evidence for differences in site average concentrations and trends in soil water DOC between sites with contrasting ecosystem properties, i.e. vegetation cover and soil type, and ii) identify the wider combination of site characteristics that best explain variation in these DOC metrics between sites. We collated soil water and deposition chemistry, soil chemistry and meteorological data from 15 long-term UK monitoring sites (1992-2010) covering a range of soils, vegetation, climate and acid deposition levels. Mineral soils under forests showed the greatest range of long-term mean DOC concentrations and trends. Regression analysis indicated that acid and sea-salt deposition, and soil sensitivity to acidification were the factors most strongly associated with spatial variation in mean DOC concentrations. Spatial variation in DOC trends were best explained by Al saturation and water flux. Overall, the sensitivity of DOC release from soil to changes in pollutant deposition could be related to the type of vegetation cover and soils chemistry properties, such as Al saturation, divalent base cation content and hydrological regime. The identification of the ecosystem properties that appear most influential in modifying DOC production and responses to long-term drivers, helps elucidate potential mechanistic explanations for differences in DOC dynamics across seemingly similar ecosystems, and points to the importance of DOC mobility in regulating its dynamics.

Assessing the reliability of peatland GPP measurements by remote sensing: From plot to landscape scale.

Estimates of peatland carbon fluxes based on remote sensing data are a useful addition to monitoring methods in these remote and precious ecosystems, but there are questions as to whether large-scale estimates are reliable given the small-scale heterogeneity of many peatlands. Our objective was to consider the reliability of models based on Earth Observations for estimating ecosystem photosynthesis at different scales using the Forsinard Flows RSPB reserve in Northern Scotland as our study site. Three sites across the reserve were monitored during the growing season of 2017. One site is near-natural blanket bog, and the other two are at different stages of the restoration process after removal of commercial conifer forestry. At each site we measured small (flux chamber) and landscape scale (eddy covariance) CO2 fluxes, small scale spectral data using a handheld spectrometer, and obtained corresponding satellite data from MODIS. The variables influencing GPP at small scale, including microforms and dominant vegetation species, were assessed using exploratory factor analysis. A GPP model using land surface temperature and a measure of greenness from remote sensing data was tested and compared to chamber and eddy covariance CO2 fluxes; this model returned good results at all scales (Pearson's correlations of 0.57 to 0.71 at small scale, 0.76 to 0.86 at large scale). We found that the effect of microtopography on GPP fluxes at the study sites was spatially and temporally inconsistent, although connected to water content and vegetation species. The GPP fluxes measured using EC were larger than those using chambers at all sites, and the reliability of the TG model at different scales was dependent on the measurement methods used for calibration and validation. This suggests that GPP measurements from remote sensing are robust at all scales, but that the methods used for calibration and validation will impact accuracy.

Effects of acidity on dissolved organic carbon in organic soil extracts, pore water and surface litters.

Over the past 30-40 years, dissolved organic carbon (DOC) concentrations have increased in soil solutions and surface waters in many acid-sensitive areas of Europe and North America. This has been linked to recovery from acidification in response to decreasing levels of atmospheric pollution. Evidence from radiocarbon dating suggests that DOC in surface waters is typically derived from recently photosynthesised organic matter such as plant litter and exudates, yet there is little information on the pH-sensitivity of organic matter solubility, or its decomposition, in litter layers and in different organic soils. Therefore the purpose of this study was to determine a) the sensitivity of DOC to acidity in different surface layers and soil types, in order to b) improve understanding of the key sources contributing to the increasing DOC trend. Such information is vital for understanding site specific characteristics contributing to inconsistencies in DOC release between catchments, and for improving predictions of carbon fluxes and budgets. Based on data collected at four established field pH-manipulation experiments in upland areas of the United Kingdom, we examined the sources, composition and acid-sensitivity of DOC export from the litter and organic soils. We found that litter generated nearly three times more DOC than the organic soils, consistent with radiocarbon evidence that recent plant inputs are a major source of DOC. Furthermore, litter derived DOC had lower specific ultraviolet light absorbance (SUVA) than organic soil DOC, suggesting greater biodegradability, and was not acid sensitive. In contrast, organic soil DOC concentrations were more strongly related to experimentally manipulated pH, implying that the mobility of this DOC may be subject to physicochemical rather than biotic controls. Our results suggest that physicochemically mediated controls on organic matter solubility may be a key driver behind the widely observed increases in surface water DOC in areas undergoing recovery from acidification.

Preservation and recovery of mangrove ecosystem carbon stocks in abandoned shrimp ponds.

Mangrove forests capture and store exceptionally large amounts of carbon and are increasingly recognised as an important ecosystem for carbon sequestration. Yet land-use change in the tropics threatens this ecosystem and its critical 'blue carbon' (carbon stored in marine and coastal habitats) stores. The expansion of shrimp aquaculture is among the major causes of mangrove loss globally. Here, we assess the impact of mangrove to shrimp pond conversion on ecosystem carbon stocks, and carbon losses and gains over time after ponds are abandoned. Our assessment is based on an intensive field inventory of carbon stocks at a coastal setting in Thailand. We show that although up to 70% of ecosystem carbon is lost when mangroves are converted to shrimp ponds, some abandoned ponds contain deep mangrove soils (>2.5 m) and large carbon reservoirs exceeding 865 t carbon per hectare. We also found a positive recovery trajectory for carbon stocks in the upper soil layer (0-15 cm) of a chronosequence of abandoned ponds, associated with natural mangrove regeneration. Our data suggest that mangrove carbon pools can rebuild in abandoned ponds over time in areas exposed to tidal flushing.

Nitric oxide production of T lymphocytes is increased in rheumatoid arthritis.

Experimental and clinical evidence for T cell involvement in the pathology of rheumatoid arthritis (RA) is compelling, and points to a local dysregulation of T cell function in the inflamed joint. Nitric oxide (NO) has been shown to regulate T cell function under physiological conditions, but overproduction of NO may contribute to lymphocyte dysfunction characteristic of RA. Several investigations in patients with RA have documented evidence of increased NO synthesis, but these studies have focused largely on macrophage-derived NO and its impact on innate immune and inflammatory responses. In this study, we set out to explore the contribution that T cells make to NO production. We find that T cells from RA patients produce >2.5 times more NO than healthy donor T cells (p<0.001). Although NO is an important physiological mediator of mitochondrial biogenesis, mitochondrial mass is similar in RA and control T cells. In contrast, increased NO production is associated with increased cytoplasmic Ca(2+) concentrations in RA T cells (p<0.001). In vitro treatment of human peripheral blood lymphocytes, or Jurkat cells with TNF increases NO production (p=0.006 and p=0.001, respectively), whilst infliximab treatment in RA patients decreases T cell derived NO production within 6 weeks of the first infusion (p=0.005). Together, these data indicate that TNF induced NO production in T lymphocytes may contribute to perturbations of immune homeostasis in RA.

Link between DOC in near surface peat and stream water in an upland catchment.

Hydrologic transport of dissolved organic carbon (DOC) from peat soils may differ to organo-mineral soils in how they responded to changes in flow, because of differences in soil profile and hydrology. In well-drained organo-mineral soils, low flow is through the lower mineral layer where DOC is absorbed and high flow is through the upper organic layer where DOC is produced. DOC concentrations in streams draining organo-mineral soils typically increase with flow. In saturated peat soils, both high and low flows are through an organic layer where DOC is produced. Therefore, DOC in stream water draining peat may not increase in response to changes in flow as there is no switch in flow path between a mineral and organic layer. To verify this, we conducted a high-resolution monitoring study of soil and stream water at an upland peat catchment in northern England. Our data showed a strong positive correlation between DOC concentrations at -1 and -5 cm depth and stream water, and weaker correlations between concentrations at -20 to -50 cm depth and stream water. Although near surface organic material appears to be the key source of stream water DOC in both peat and organo-mineral soils, we observed a negative correlation between stream flow and DOC concentrations instead of a positive correlation as DOC released from organic layers during low and high flow was diluted by rainfall. The differences in DOC transport processes between peat and organo-mineral soils have different implications for our understanding of long-term changes in DOC exports. While increased rainfall may cause an increase in DOC flux from peat due to an increase in water volume, it may cause a decrease in concentrations. This response is contrary to expected changes in DOC exports from organo-mineral soils, where increase rainfall is likely to result in an increase in flux and concentration.

Buffering of recovery from acidification by organic acids.

In the United Kingdom, as in other regions of Europe and North America, recent decreases in surface water sulphate concentrations, due to reduced sulphur emissions, have coincided with marked increases in dissolved organic carbon (DOC) concentrations. Since many of the compounds comprising DOC are acidic, the resulting increases in organic acidity may have the potential to offset the benefits of a decrease in mineral (sulphate) acidity. To test this, we used a triprotic model of organic acid dissociation to estimate the proportional organic acid buffering of reduced mineral acidity as measured in the 22 lakes and streams monitored by the UK Acid Waters Monitoring Network. For an average non-marine sulphate decrease of 30 mueq l(-1) over 15 years from 1988-2003, we estimate that around 28% was counterbalanced by rising strong organic acids, 20% by rising alkalinity (partly attributable to an increase in weak organic acids), 11% by falling inorganic aluminium and 41% by falling non-marine base cations. The situation is complicated by a concurrent decrease in marine ion concentrations, and the impact this may have had on both DOC and acidity, but results clearly demonstrate that organic acid increases have substantially limited the amount of recovery from acidification (in terms of rising alkalinity and falling aluminium) that have resulted from reducing sulphur emissions. The consistency and magnitude of sulphate and organic acid changes are consistent with a causal link between the two, possibly due to the effects of changing acidity, ionic strength and aluminium concentrations on organic matter solubility. If this is the case, then organic acids can be considered effective but partial buffers to acidity change in organic soils, and this mechanism needs to be considered in assessing and modelling recovery from acidification, and in defining realistic reference conditions. However, large spatial variations in the relative magnitude of organic acid and sulphate changes, notably for low-deposition sites in northwestern areas where organic acid increases apparently exceed non-marine sulphate decreases, suggest that additional factors, such as changes in sea-salt deposition and climatic factors, may be required to explain the full magnitude of DOC increases in UK surface waters.

The influence of organic acids in relation to acid deposition in controlling the acidity of soil and stream waters on a seasonal basis.

Much uncertainty still exists regarding the relative importance of organic acids in relation to acid deposition in controlling the acidity of soil and surface waters. This paper contributes to this debate by presenting analysis of seasonal variations in atmospheric deposition, soil solution and stream water chemistry for two UK headwater catchments with contrasting soils. Acid neutralising capacity (ANC), dissolved organic carbon (DOC) concentrations and the Na:Cl ratio of soil and stream waters displayed strong seasonal patterns with little seasonal variation observed in soil water pH. These patterns, plus the strong relationships between ANC, Cl and DOC, suggest that cation exchange and seasonal changes in the production of DOC and seasalt deposition are driving a shift in the proportion of acidity attributable to strong acid anions, from atmospheric deposition, during winter to predominantly organic acids in summer.

Nitric oxide, chronic inflammation and autoimmunity.

Whilst many physiological functions of nitric oxide (NO) have been revealed so far, recent evidence proposes an essential role for NO in T lymphocyte activation and signal transduction. NO acts as a second messenger, activating soluble guanyl cyclase and participating in signal transduction pathways involving cyclic GMP. NO modulates mitochondrial events that are involved in apoptosis and regulates mitochondrial biogenesis in many cell types, including lymphocytes. Several studies undertaken on patients with RA and SLE have documented increased endogenous NO synthesis, although the effects of NO may be distinct. Here, we discuss recent evidence that NO contributes to T cell dysfunction in both SLE and RA by altering multiple signaling pathways in T cells. Although NO may play a physiological role in lymphocyte cell signaling, its overproduction may perturb T cell activation, differentiation and effector responses, each of which may contribute in different ways to the pathogenesis of autoimmunity.

Managing peatland vegetation for drinking water treatment.

Peatland ecosystem services include drinking water provision, flood mitigation, habitat provision and carbon sequestration. Dissolved organic carbon (DOC) removal is a key treatment process for the supply of potable water downstream from peat-dominated catchments. A transition from peat-forming Sphagnum moss to vascular plants has been observed in peatlands degraded by (a) land management, (b) atmospheric deposition and (c) climate change. Here within we show that the presence of vascular plants with higher annual above-ground biomass production leads to a seasonal addition of labile plant material into the peatland ecosystem as litter recalcitrance is lower. The net effect will be a smaller litter carbon pool due to higher rates of decomposition, and a greater seasonal pattern of DOC flux. Conventional water treatment involving coagulation-flocculation-sedimentation may be impeded by vascular plant-derived DOC. It has been shown that vascular plant-derived DOC is more difficult to remove via these methods than DOC derived from Sphagnum, whilst also being less susceptible to microbial mineralisation before reaching the treatment works. These results provide evidence that practices aimed at re-establishing Sphagnum moss on degraded peatlands could reduce costs and improve efficacy at water treatment works, offering an alternative to 'end-of-pipe' solutions through management of ecosystem service provision.

Pathways of T cell activation and terminal differentiation in chronic inflammation.

Immune and inflammatory responses are governed by antigen-specific T cells, whose activation, differentiation and effector function are induced by signals delivered via the T cell antigen receptor (TCR) and by costimulatory and cytokine receptors. The molecular events leading to the activation of naïve T cells have been extensively studied and are well characterized. Much less is known about the molecular and biochemical events regulating the activation of T cells in chronic inflammatory diseases such as rheumatoid arthritis (RA). This review examines the current state of knowledge of T cell activation in chronic inflammation, focusing on RA, and summarizes experimental data which indicate that the chronic inflammatory process may profoundly affect TCR and cytokine signal transduction pathways. We present evidence suggesting that in chronic inflammation, the antigen-driven TCR-mediated processes are attenuated, while cytokine-driven effector responses are sustained or even enhanced. The possible implications of this inbalance are discussed.

Simulated climate change impact on summer dissolved organic carbon release from peat and surface vegetation: implications for drinking water treatment.

Uncertainty regarding changes in dissolved organic carbon (DOC) quantity and quality has created interest in managing peatlands for their ecosystem services such as drinking water provision. The evidence base for such interventions is, however, sometimes contradictory. We performed a laboratory climate manipulation using a factorial design on two dominant peatland vegetation types (Calluna vulgaris and Sphagnum Spp.) and a peat soil collected from a drinking water catchment in Exmoor National Park, UK. Temperature and rainfall were set to represent baseline and future conditions under the UKCP09 2080s high emissions scenario for July and August. DOC leachate then underwent standard water treatment of coagulation/flocculation before chlorination. C. vulgaris leached more DOC than Sphagnum Spp. (7.17 versus 3.00 mg g(-1)) with higher specific ultraviolet (SUVA) values and a greater sensitivity to climate, leaching more DOC under simulated future conditions. The peat soil leached less DOC (0.37 mg g(-1)) than the vegetation and was less sensitive to climate. Differences in coagulation removal efficiency between the DOC sources appears to be driven by relative solubilisation of protein-like DOC, observed through the fluorescence peak C/T. Post-coagulation only differences between vegetation types were detected for the regulated disinfection by-products (DBPs), suggesting climate change influence at this scale can be removed via coagulation. Our results suggest current biodiversity restoration programmes to encourage Sphagnum Spp. will result in lower DOC concentrations and SUVA values, particularly with warmer and drier summers.

Inhibitor of kappa B epsilon (IκBε) is a non-redundant regulator of c-Rel-dependent gene expression in murine T and B cells.

Inhibitors of kappa B (IκBs) -α, -ß and -ε effect selective regulation of specific nuclear factor of kappa B (NF-κB) dimers according to cell lineage, differentiation state or stimulus, in a manner that is not yet precisely defined. Lymphocyte antigen receptor ligation leads to degradation of all three IκBs but activation only of subsets of NF-κB-dependent genes, including those regulated by c-Rel, such as anti-apoptotic CD40 and BAFF-R on B cells, and interleukin-2 (IL-2) in T cells. We report that pre-culture of a mouse T cell line with tumour necrosis factor-α (TNF) inhibits IL-2 gene expression at the level of transcription through suppressive effects on NF-κB, AP-1 and NFAT transcription factor expression and function. Selective upregulation of IκBε and suppressed nuclear translocation of c-Rel were very marked in TNF-treated, compared to control cells, whether activated via T cell receptor (TCR) pathway or TNF receptor. IκBε associated with newly synthesised c-Rel in activated cells and, in contrast to IκBα and -ß, showed enhanced association with p65/c-Rel in TNF-treated cells relative to controls. Studies in IκBε-deficient mice revealed that basal nuclear expression and nuclear translocation of c-Rel at early time-points of receptor ligation were higher in IκBε-/- T and B cells, compared to wild-type. IκBε-/- mice exhibited increased lymph node cellularity and enhanced basal thymidine incorporation by lymphoid cells ex vivo. IκBε-/- T cell blasts were primed for IL-2 expression, relative to wild-type. IκBε-/- splenic B cells showed enhanced survival ex vivo, compared to wild-type, and survival correlated with basal expression of CD40 and induced expression of CD40 and BAFF-R. Enhanced basal nuclear translocation of c-Rel, and upregulation of BAFF-R and CD40 occurred despite increased IκBα expression in IκBε-/- B cells. The data imply that regulation of these c-Rel-dependent lymphoid responses is a non-redundant function of IκBε.

Rheumatoid arthritis: a disease of chronic, low-amplitude signals transduced through T cell antigen receptors?

Technology has advanced to the stage where it is now possible to identify genes that confer low to moderate risk of developing autoimmune diseases such as rheumatoid arthritis (RA). This has been facilitated by the growing appreciation that these hard to detect genetic signals can only be defined in large cohorts of well characterized patients. In RA, the association between disease susceptibility and genes encoded within the MHC has been known for decades. Recent studies have identified several new candidate genes that provide further insights into the molecular nature of aberrant immune responses in chronic inflammatory diseases. Here, we describe some of these new genes. Based on their known functions we propose that in a subgroup of patients with RA inheritance of allelic variants at distinct loci could lead to dysregulation of adaptive immune responses characterized by chronic, low-amplitude signaling transduced by antigen T cell receptors.

Suppression of dissolved organic carbon by sulfate induced acidification during simulated droughts.

The relationship between dissolved organic carbon (DOC) and the acidification of soils and freshwaters by sulfate (SO4(2-)) has been a topic of great debate over the last few decades. Most interest has focused on long-term acidification. Few have considered the influence of episodic drought-induced acidification in peatlands on DOC mobility, even through the increased acidity and ionic strength associated with the oxidation of reduced sulfur to SO4(2-) are known to reduce DOC solubility. Reduced DOC concentrations during droughts have often been attributed to: (i) reduced hydrological export; (ii) physicochemical changes in the peat structure; or (iii) changes in the biological production and/or consumption of DOC. Our experimental drought simulations on peat cores showed that SO4(2-) induced acidification reduced DOC concentrations during droughts. However, the relationships between SO4(2-)/pH/ ionic strength and DOC were only apparent when the reductions in observed DOC were expressed as a fraction of the estimated DOC concentration in the absence of SO4(2-), which were derived from soil depth, temperature, and watertable data. This analysis showed that a pH fall from 4.3 to 3.5, due to a SO4(2-) rise from < 2.5 to 35 mg L(-1), caused a 60% reduction in DOC concentrations. In contrast, poor correlations were recorded between S042-/pH/ionic strength and the observed DOC data. As DOC both influences acidity and is influenced by acidity, the relative change in DOC needed to be considered to disentangle the effect of inputs of mineral acids into a system naturally dominated by variable concentrations of organic acids.

T cell receptor zeta reconstitution fails to restore responses of T cells rendered hyporesponsive by tumor necrosis factor alpha.

Expression and function of the antigen T cell receptor (TCR) play a central role in regulating immune responsiveness. Accordingly, targeting the expression of TCRalphabeta or its associated CD3 subunits profoundly influences T cell development and adaptive immunity. Down-regulation of the invariant TCRzeta chain has been documented in a wide variety of chronic inflammatory and infectious diseases, and is thought to contribute to the paradoxical immune suppression observed in these diseases. Previously, we reported that prolonged exposure of T cell hybridoma clones to tumor necrosis factor alpha (TNF) induces nondeletional and reversible hyporesponsiveness to TCR engagement, associated with down-regulation of TCRzeta chain expression, impaired TCR/CD3 complex assembly, and attenuation of TCR-induced membrane proximal tyrosine phosphorylation. Here, we have tested whether receptor specific T cell responses are rescued in TNF-treated T cell hybridomas by retroviral-mediated expression of zeta-chimeric (C2zeta) receptors or wild-type TCRzeta. Expression of C2zeta receptors at the cell surface is relatively refractory to chronic TNF stimulation. However, C2zeta receptor function depends on association with endogenous TCRzeta chains, whose expression is down-regulated by TNF, and so C2 receptor specific responses are attenuated in TNF-treated T cells. Unexpectedly, overexpression of wild-type TCRzeta maintains cell surface TCR/CD3 complex expression but fails to rescue receptor proximal signaling in TNF-treated T cells, suggesting the existence of hitherto unrecognized mechanisms through which TNF regulates T cell responsiveness. We provide additional evidence that TNF also uncouples distal TCR signaling pathways independently of its effects on TCRzeta expression.