Organic matter pools and nutrient cycling in different coffee production systems in the Brazilian Cerrado

Agroforestry and organic systems have been used to reduce the negative effects that conventional coffee cultivation has on soils. In this work, ¹³C-CPMAS-NMR, Fourier transform infrared spectroscopy, elemental composition, classical humus fractionation and the soil fertility status were used to evaluate the impact of these three systems on a Latosol from the Brazilian Cerrado. Continuous input of tree residues promoted changes to the soil organic matter with increase in total organic carbon, humic acids (HA) and light organic matter, mainly in the topsoil. Available P and cation exchange capacity were also increased and the acidity status decreased in the agroforestry system. Moreover, HA from the agroforestry were enriched in O-alkyl C, O-di-alkyl C and alkyl C groups and the organic system resulted in HA richer in carboxyl groups. The conventional system resulted in greater aromatic and methoxyl participation, and lower phenol groups. HA from the agroforestry system were richer in easily degradable structures and the chemical fractionation demonstrated a decrease in both recalcitrant fractions, allowing for a more conservative and sustainable management of soil fertility. The modifications were not as evident in the organic system, probably due to the low organic fertilizer input.     

Rhizobacteria-mediated Induced Systemic Resistance: Triggering, Signalling and Expression

Selected strains of rhizosphere bacteria reduce disease by activating a resistance mechanism in the plant named rhizobacteria-mediated induced systemic resistance (ISR). Rhizobacteria-mediated ISR resembles pathogen-induced systemic acquired resistance (SAR) in that both types of induced resistance render uninfected plant parts more resistant towards a broad spectrum of plant pathogens. Some rhizobacteria trigger the salicylic acid (SA)-dependent SAR pathway by producing SA at the root surface. In other cases, rhizobacteria trigger a different signalling pathway that does not require SA. The existence of a SA-independent ISR pathway has been demonstrated in Arabidopsis thaliana. In contrast to pathogen-induced SAR, ISR induced by Pseudomonas fluorescens WCS417r is independent of SA accumulation and pathogenesis-related (PR) gene activation but, instead, requires responsiveness to the plant hormones jasmonic acid (JA) and ethylene. Mutant analyses showed that ISR follows a novel signalling pathway in which components from the JA and ethylene response are successively engaged to trigger a defensive state that, like SAR, is controlled by the regulatory factor NPR1. Interestingly, simultaneous activation of both the JA/ethylene-dependent ISR pathway and the SA-dependent SAR pathway results in an enhanced level of protection. Thus combining both types of induced resistance provides an attractive tool for the improvement of disease control. This review focuses on the current status of our research on triggering, signalling, and expression of rhizobacteria-mediated ISR in Arabidopsis.     

Estimation of sensitivity and specificity of three conditionally dependent diagnostic tests in the absence of a gold standard

This article presents a model to evaluate the accuracy of diagnostic tests. Data from three tests for the detection of EF-positive Streptococcus suis serotype 2 strains in sows were analyzed. The data were collected in a field study in the absence of a gold standard, that is, the true disease status (noninfected or infected) of the tested animals was unknown. Two tests were based on a polymerase chain reaction (PCR); one test was applied to a tonsil swab (taken from the live animal), and the other test was applied to the whole tonsil (collected at slaughter). The third test was based on a bacterial examination (BE) of the whole tonsil. To reduce experimental cost BE was performed only for a subset of the animals in the sample. The model allows for dependence between tests, conditional upon the unknown true disease status of the animals. Accuracy was expressed in terms of sensitivity and specificity of the tests. A Bayesian analysis was performed that incorporated prior information about the accuracy of the tests. The model parameters have a simple interpretation and specification of priors is straightforward. Posterior inference was carried out with Markov chain Monte Carlo (MCMC) methods, employing the Gibbs sampler, as implemented in the WinBUGS program. Different parameterizations to allow for selection and missing values, use of different priors, practical problems in the analysis, and some interesting issues in a joint analysis of the binary (positive or negative) results of PCR and BE and two additional continuous enzyme-linked immunosorbent assays (ELISA) are discussed.     

Plasma levels of six carotenoids in nine European countries: report from the European Prospective Investigation into Cancer and Nutrition (EPIC)

BACKGROUND: In addition to their possible direct biological effects, plasma carotenoids can be used as biochemical markers of fruit and vegetable consumption for identifying diet-disease associations in epidemiological studies. Few studies have compared levels of these carotenoids between countries in Europe. OBJECTIVE: Our aim was to assess the variability of plasma carotenoid levels within the cohort of the European Prospective Investigation into Cancer and Nutrition (EPIC). METHODS: Plasma levels of six carotenoids--alpha-carotene, beta-carotene, beta-cryptoxanthin, lycopene, lutein and zeaxanthin--were measured cross-sectionally in 3043 study subjects from 16 regions in nine European countries. We investigated the relative influence of gender, season, age, body mass index (BMI), alcohol intake and smoking status on plasma levels of the carotenoids. RESULTS: Mean plasma level of the sum of the six carotenoids varied twofold between regions (1.35 micromol l(-1) for men in Malm?, Sweden vs. 2.79 micromol l(-1) for men in Ragusa/Naples, Italy; 1.61 micromol l(-1) for women in The Netherlands vs. 3.52 micromol l(-1) in Ragusa/Naples, Italy). Mean levels of individual carotenoids varied up to fourfold (alpha-carotene: 0.06 micromol l(-1) for men in Murcia, Spain vs. 0.25 micromol l(-1) for vegetarian men living in the UK). In multivariate regression analyses, region was the most important predictor of total plasma carotenoid level (partial R(2)=27.3%), followed by BMI (partial R(2)=5.2%), gender (partial R(2)=2.7%) and smoking status (partial R(2)=2.8%). Females had higher total carotenoid levels than males across Europe. CONCLUSIONS: Plasma levels of carotenoids vary substantially between 16 different regions in Italy, Greece, Spain, France, Germany, the UK, Sweden, Denmark and The Netherlands. Compared with region of residence, the other demographic and lifestyle factors and laboratory measurements have limited predictive value for plasma carotenoid levels in Europe.     

Spatial and temporal variation of muddy floods in central Belgium, off-site impacts and potential control measures

Numerous villages in the European loess belt are confronted with floods caused by runoff from agricultural land. Seventy-nine percent of the municipalities in central Belgium experienced at least one muddy flood during the last decade. Of these flooded municipalities, 22% have been affected more than 10 times during this period. Twenty municipalities have been selected for a detailed analysis. A database of 367 locations affected by muddy floods has been compiled, and the connectivity between cultivated areas and inhabited zones could be assessed for 100 flooded locations. Roads and drainage network facilitate runoff transfer between cultivated and inhabited areas in 64% of cases. Three types of areas producing muddy floods have been identified: hillslopes (1–30 ha) without thalweg where runoff is generally dominated by sheet flow; small catchments (10–300 ha) characterised by runoff concentration in the thalweg and medium catchments (100–300 ha) with multiple thalwegs dominated by concentrated runoff. About 90% of muddy floods are generated on hillslopes and in small catchments. A critical area–slope threshold for triggering muddy floods has been computed for hillslopes. A logistic regression shows that muddy floods are generated in small and medium catchments with 99% probability after 43 mm rainfall. Rainfall depths required to trigger muddy floods are lower in May and June (25 ±12 mm) than between July and September (46 ± 20 mm), because of different surface conditions (crusting, roughness and crop cover). Each year, muddy floods lead to a total societal cost of 16 × 10⁶–172 × 10⁶ € in central Belgium, depending on the extent and intensity of thunderstorms and monetary values damaged. Recent datasets suggest that the phenomenon is becoming more frequent in central Belgium, because of land consolidation, urban sprawl and expansion of row crops, sown in spring, at the expense of winter cereals. The huge costs induced by muddy floods justify the installation of erosion control measures. It is suggested to install a grassed buffer strip at the downslope edge of cultivated hillslopes to protect houses and roads. In small and medium catchments, it is preferred to install a grassed waterway and earthen dams in the thalweg.     

Intestinal translocation of Streptococcus suis type 2 EF+ in pigs

Sepsis with subsequent multisystem organ failure after translocation of bacteria from the gut is a serious risk associated with stress situations. We showed that intestinal bacterial translocation could be one of the pathways for pathogenic Streptococcus suis infections in the pig. In 24 piglets weighing 10-14 kg, free of the extracellular factor (EF+) producing phenotype of S. suis serotype 2, a silicon canula was placed in the proximal jejunum to enable intestinal inoculation and bypassing the upper alimentary tract. The pigs were individually housed. After stress induction in 18 pigs by means of a truck drive in individual cages for 1h, pigs were inoculated through the intestinal canula either with S. suis type 2 EF+ or with growth medium only, and put back in their original housing. The six not transported pigs were also inoculated with the same strain. To prevent oral self-infection, faeces were collected in a bag that was glued around the anus. Clinical and behavioral symptoms were recorded for 72 h post inoculation, and then the animals were sacrificed for pathological and bacteriological examination. In three animals, the inoculation strain was re-isolated from mesenterial lymph nodes and typically affected organs. No S. suis type 2 EF+ was detected by specific polymerase chain reaction (PCR) in any of the tonsil-swabs and -homogenates. We concluded that infection of the organs had taken place after bacterial translocation out of the gut and that the intestinal tract can be a porte d'entree for S. suis type 2 EF+.     

Parathyroid gland function in the uremic rabbit

Rabbits with renal failure have been reported to be hypercalcemic and to have decreased parathyroid hormone (PTH) concentrations. Thus, it would seem that uremic rabbits are resistant to secondary hyperparathyroidism (HPT). The work reported here was designed to investigate parathyroid gland function in uremic rabbits and the effect of diets with different calcium (Ca) and phosphorus (P) content. The relationship between PTH and ionized calcium (Ca2+), parathyroid gland size and parathyroid cell cycle were studied in three groups of rabbits: Group I, rabbits with normal renal function on a standard diet (Ca = 1.2%, P = 0.6%); Group II, partially nephrectomized rabbits on a standard diet; and Group III, partially nephrectomized rabbits on a low Ca (0.6%)-high P (1.2%) diet. Group I rabbits had baseline Ca2+ = 1.71 +/- 0.05 mmol/l and PTH = 26.9 +/- 3.2 pg/ml. During hypo- and hypercalcemic stimulation PTH reached maximal values (PTHmax) of 94.4 +/- 5.5 pg/ml and minimal concentrations (PTHmin) of 3.2 +/- 0.2 pg/ml. Rabbits from Group II were hypercalcemic (baseline Ca2+ = 2.03 +/- 0.06 mmol/l) and had very low PTH levels (1.7 +/- 0.5 pg/ml); however, they reached a PTHmax that was similar to Group I, 92 +/- 8.7 pg/ml. Group III rabbits were hypocalcemic (baseline Ca2+ = 1.22 +/- 0.08 mmol/l) and had very high basal PTH levels (739 +/- 155 pg/ml). Their PTHmax and PTHmin were 801 +/- 169.4 pg/ml and 102.2 +/- 22.2 pg/ml, respectively. Both parathyroid gland size and parathyroid cell proliferation were increased in Group III. In conclusion, our results show that the Ca and P content of the diet markedly influence PTH secretion in the uremic rabbit and that when placed on a low Ca-high P diet uremic rabbits develop secondary HPT.     

Exploring the potential of intersectoral partnerships to improve the position of farmers in global agrifood chains: findings from the coffee sector in Peru

Despite their recent proliferation in global agricultural commodity chains, little is known about the potential of intersectoral partnerships to improve the position of smallholder farmers and their organizations. This article explores the potential of partnerships by developing a conceptual approach based on the sustainable livelihoods and linking farmers to market perspectives, which is applied in an exploratory study to six partnerships in the coffee sector in Peru. It is concluded that partnerships stimulate the application of standards to receive market access and therefore emphasize human capital development of farmers to facilitate certification. By transferring knowledge to farmers, partnerships present a new source of technological change, which, in combination with certification, holds potential for improved environmental management and price premiums for producers. However, the emphasis on certification results in a comparatively narrow target group of farmers and is associated with high financial burdens for producer organizations. At the same time, other assets of producer organizations are often not strengthened sufficiently for them to operate successfully without further external support. This suggests that preparing producers for certification is prioritized over empowering organizations toward self-dependence.     

Effects of rock fragments on physical degradation of cultivated soils by rainfall

To understand better the role of rock fragments in soil and water conservation processes, the effects of rock fragments in maintaining a favourable soil structure and thus also in preventing physical degradation of tilled soils was studied. Laboratory experiments were conducted to investigate the effects of rock fragment content, rock fragment size, initial soil moisture content of the fine earth and surface rock fragment cover on soil subsidence by rainfall (i.e. change in bulk density by one or more cycles of wetting and drying). A total of 15 rainfall simulations (cumulative rainfall, 192.5 mm; mean intensity, 70 mm h⁻¹) were carried out. Before and after each rainfall application the surface elevation of a 19-cm thick plough layer was measured with a laser microrelief meter. In all experiments, the bulk density of the fine earth increased with applied rainfall volume to reach a maximum value at about 200 mm of cumulative rainfall. From the experimental results it was concluded that the subsidence rate decreased sharply for soils containing more than 0.50 kg kg⁻¹ rock fragments, irrespective of rock fragment size. Fine earth bulk densities were negatively related to rock fragment content beyond a threshold value of 0.30 kg kg⁻¹ for small rock fragments (1.7–2.7 cm) and 0.50 kg kg⁻¹ for large rock fragments (7.7 cm). Initial soil moisture content influenced subsidence only in the initial stage of the experiments, when some swelling occurred in the dry soils. Surface rock fragment cover had no significant effect on subsidence of the plough layer. Therefore, subsidence of the plough layer in these experiments appears to be mainly due to changing soil strength upon drainage rather than the result of direct transfer of kinetic energy from falling drops. The relative increase in porosity of the fine earth as well as the absolute increase in macroporosity with rock fragment content will cause deeper penetration of rainfall into the soil, resulting in water conservation. Therefore, crushing of large rock fragments into smaller ones is to be preferred over removal of rock fragments from the plough layer.