Quantifying regulating ecosystem services with increased tree densities on European Farmland

Agroforestry systems have been compared to agricultural and forestry alternatives, providing a land-use solution for additional environmental benefits while maintaining similar levels of productivity. However, there is scarce research assessing such patterns across a pan-European scale using a common methodology. This study aims to improve our understanding of the role of trees in three different regulating ecosystem services—(1) soil erosion, (2) nitrate leaching and (3) carbon sequestration—in traditional and innovative agroforestry systems in Europe through a consistent modeling approach. The systems’ assessment spans environmentally from the Mediterranean environmental region in Portugal to the Continental environmental region in Switzerland and Germany to the Atlantic environmental region in the United Kingdom. Modeled tree densities were compared in the different land-use alternatives, ranging from zero (agriculture with only crops or pasture) to forestry (only trees). The methodology included the use of a biophysical model (Yield-SAFE) where the quantification of the environmental benefits was integrated. Results show a consistent improvement of regulating ecosystem services can be expected when introducing trees in the farming landscapes in different environmental regions in Europe. For all the systems, the forestry alternatives presented the best results in terms of a decrease in soil erosion of 51% (±29), a decrease of nearly all the nitrate leaching (98% ± 1) and an increase in the carbon sequestration of up to 238 Mg C ha−1 (±140). However, these alternatives are limited in the variety of food, energy and/or materials provided. On the other hand, from an arable or pure-pasture alternative starting point, an increase in agroforestry tree density could also be associated with a decrease in soil erosion of up to 25% (±17), a decrease in nitrates leached of up to 52% (±34) and an increase in the carbon sequestered of 163 Mg C ha−1 (±128) while at the same time ensuring the same levels of biomass growth and an increase in product diversification.We acknowledge the financial support provided by the Portuguese Foundation for Science and Technology (FCT) through the scholarship (SFRH/BD/52691/2014) and the European Community's Seventh Framework Programme under Grant Agreement No. 613520 (Project AGFORWARD). This research was funded by the Forest Research Centre, a research unit funded by Funda??o para a Ci?ncia e a Tecnologia I.P. (FCT), Portugal (UIDB/00239/2020)

Integrating belowground carbon dynamics into Yield-SAFE, a parameter sparse agroforestry model

Agroforestry combines perennial woody elements (e.g. trees) with an agricultural understory (e.g. wheat, pasture) which can also potentially be used by a livestock component. In recent decades, modern agroforestry systems have been proposed at European level as land use alternatives for conventional agricultural systems. The potential range of benefits that modern agroforestry systems can provide includes farm product diversification (food and timber), soil and biodiversity conservation and carbon sequestration, both in woody biomass and the soil. Whilst typically these include benefits such as food and timber provision, potentially, there are benefits in the form of carbon sequestration, both in woody biomass and in the soil. Quantifying the effect of agroforestry systems on soil carbon is important because it is one means by which atmospheric carbon can be sequestered in order to reduce global warming. However, experimental systems that can combine the different alternative features of agroforestry systems are difficult to implement and long-term. For this reason, models are needed to explore these alternatives, in order to determine what benefits different combinations of trees and understory might provide in agroforestry systems. This paper describes the integration of the widely used soil carbon model RothC, a model simulating soil organic carbon turnover, into Yield-SAFE, a parameter sparse model to estimate aboveground biomass in agroforestry systems. The improvement of the Yield-SAFE model focused on the estimation of input plant material into soil (i.e. leaf fall and root mortality) while maintaining the original aspiration for a simple conceptualization of agroforestry modeling, but allowing to feed inputs to a soil carbon module based on RothC. Validation simulations show that the combined model gives predictions consistent with observed data for both SOC dynamics and tree leaf fall. Two case study systems are examined: a cork oak system in South Portugal and a poplar system in the UK, in current and future climate. (c) 2017, Springer Science+Business Media B.V.European Commission through the AGFORWARD FP7 research Project (contract 613520), Forest Research Center strategic Project (PEst OE/AGR/UI0239/2014), the Portuguese Foundation for Science and Technology (FCT) fellowships SFRH/BD/52691/2014 and SFRH/BPD/96475/2013, XUNTA DE GALICIA, Consellería de Cultura, Educación e Ordenación Universitaria (“Programa de axudas á etapa posdoutoral”) (contract ED481B 2016/071-0

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Isolation of Coxiella burnetii from serum of patients with acute Q fever

Worldwide there are few isolate collections of the intracellular bacterium Coxiella burnetii, due to the difficulties associated with working with the organism and the scarcity of suitable samples from which to attempt isolation. Particularly lacking are isolates from acute Q fever patients. The aim of this study was to evaluate whether the serum samples taken from patients with confirmed acute Q fever during the early stage of their disease represented a potential source of viable C. burnetii. Isolation was attempted from 65 of these samples by inoculation of the serum into Vero cell culture and was successful in 36 cases (55%). This high success rate was likely due to extended incubation of up to twelve weeks of the inoculated cultures, allowing the growth of the organism to levels detectable by PCR. Retrospective analysis of the time the sera was stored prior to inoculation into culture demonstrated that C. burnetii remained viable for 224. days in samples stored refrigerated and 371. days in samples stored frozen at - 20. °C. These results demonstrate that standard serum samples taken from acute Q fever patients are a valuable source of new isolates of C. burnetii, with no special handling of the specimens required to maintain the organism's viability

Comparative sensitivity of four different cell lines for the isolation of Coxiella burnetii

Coxiella burnetii is an obligate intracellular bacterium that causes the disease Q-fever. This is usually diagnosed by serology (immunofluorescence assay) and/or PCR detection of C. burnetii DNA. However, neither of these methods can determine the viability of the bacterium. Four different cell lines were compared for their ability to amplify very low numbers of viable C. burnetii. Two different isolates of C. burnetii were used. For the Henzerling isolate, DH82 (dog macrophage) cells were the most sensitive with an ID 50 (dose required to infect 50% of cell cultures) of 14.6 bacterial copies. For the Arandale isolate, Vero (monkey epithelial) cells were the most sensitive with an ID 50 of less than one bacterium in a 100-μL inoculum. The Vero cell line appeared highly useful as vacuoles could be seen microscopically in unstained infected cells. The findings of this study favour the use of Vero and DH82 tissue culture cell lines for isolation and growth of C. burnetii in vitro. The other cell lines, XTC-2 and L929, were less suitable

A comparison of methods for extracting DNA from Coxiella burnetii as measured by a duplex qPCR assay

To determine the optimal DNA extraction method for the detection of Coxiella burnetii including the small-cell variant (SCV) by real-time PCR (qPCR) in clinical samples. Methods and Results: A duplex qPCR detecting two Coxiella burnetii gene targets (com1 and IS1111a genes) was developed. Each target in this PCR had a sensitivity of one copy number per reaction. DNA extraction methods were compared on spiked negative samples and included a silica column kit, a chloroform separation prior to a silica column method and a chloroform/phenol separation and DNA precipitation method. Conclusions: The silica column extraction method was more efficient at recovering C. burnetii DNA, from large-cell and small-cell variants, than a chloroform or chloroform/phenol method. The silica column method was useful on spiked human samples including serum, buffy coat and bone marrow samples. Significance and impact of study: This study demonstrated that a simple column kit method is efficient to use for the detection of C. burnetii in clinical samples including the SCV