Evidence of differential spreading events of grapevine pinot Gris virus in Italy using datamining as a tool

European Journal of Plant Pathology - Since its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus) has now been detected in most grape-growing countries. So far, little is known...     

A model describing the interactions between anaerobic microbiology and geochemistry in a soil amended with glucose and nitrate

Under anaerobic conditions, microbes closely interact with geochemical reactions and can have an impact on the soil, the deep vadose zone, the underlying aquifer and the atmosphere. We have designed a model combining anaerobic microbial activities with geochemical reactions in the soil, and assessed it in batch experiments. The model describes the dynamics of six functional microbial communities, their decomposition after death, and the catabolism of carbohydrates through denitrification, dissimilatory NH₄⁺ production, Fe(III) reduction, fermentation, acetogenesis, and SO₄^2– reduction. It was combined with a model that thermodynamically describes acid–base, reduction–oxidation and complexation reactions in solution, and kinetic precipitation and dissolution. Batch incubations were done on a Calcic Cambisol, either without amendment, or after supplying (i) glucose or (ii) glucose and NO₃^–. Gases, mineral cations and anions, glucose, fatty acids and alcohols were measured during incubation. Net production of CO₂ was similar for both glucose treatments, about 40 times larger than in the control. For the glucose treatments, the main microbial activities were fermentation, acetogenic transformation of ethanol, and oxidation of H₂. When the soil was enriched with NO₃^–, no H₂ was produced, and microbial activities were rapidly inhibited by NO₂^–. The model shows these trends as well as geochemical characteristics including pH and reduction–oxidation potential.     

Experimental infection of Pacific oyster Crassostrea gigas spat by ostreid herpesvirus 1: demonstration of oyster spat susceptibility

ABSTRACT: In 2008 and 2009, acute mortalities occurred in France among Pacific cupped oyster, Crassostrea gigas, spat. Different hypothesis including the implication of environmental factors, toxic algae and/or pathogens have been explored. Diagnostic tests indicated that OsHV-1 including a particular genotype, termed OsHV-1 μVar, was detected in most of samples and especially in moribund oysters with the highlighting of virus particles looking like herpes viruses by TEM examination. In this study, an experimental protocol to reproduce OsHV-1 infection in laboratory conditions was developed. This protocol was based on the intramuscular injection of filtered (0.22 μm) tissue homogenates prepared from naturally OsHV-1 infected spat collected on French coasts during mortality outbreaks in 2008. Results of the experimental trials showed that mortalities were induced after injection. Moreover, filtered tissue homogenates induced mortalities whereas the same tissue homogenates exposed to an ultraviolet (UV) treatment did not induce any mortality suggesting that oyster spat mortalities require the presence of a UV sensitive agent. Furthermore, analysis of injected oyster spat revealed the detection of high amounts of OsHV-1 DNA by real-time quantitative PCR. Finally, TEM analysis demonstrated the presence of herpes virus particles. The developed protocol allowed to maintain sources of infective virus which can be useful for the development of further studies concerning the transmission and the development of OsHV-1 infection.     

Insights on the association between somatic aneuploidy and ostreid herpesvirus 1 detection in the oysters Crassostrea gigas,C. angulata and their F1 hybrids

Cytogenetic abnormalities associated with viral infections, including from viruses of the Herpesvirales order, have been reported in vertebrate species. Ostreid herpesvirus 1 (OsHV‐1) has been detected worldwide during mortality outbreaks of the Pacific oyster Crassostrea gigas. On the other hand, a high proportion of aneuploid cells in somatic tissues have been observed in C. gigas. In this study, we analysed the putative association between aneuploidy levels and the detection of OsHV‐1 in gills of C. gigas, the Portuguese oyster C. angulata and their F1 hybrids cultured in Ria Formosa (Portugal). OsHV‐1 was detected by PCR in 5.4% of the total of oysters analysed (n = 111) namely in 11.1%, 8.0% and 1.7% of C. gigas, C. angulata and F1 hybrid respectively. Sequencing analysis of a viral fragment amplified with the C2/C6 primer pair revealed a high similarity with the OsHV‐1 reference type. Moreover, in situ hybridization confirmed the presence of OsHV‐1 in gill tissue. Oysters where OsHV‐1 was detected had a significantly higher mean percentage of aneuploid cells (25%) than the ones where the virus was not detected (18%). However, the overall low percentage of positive samples contrasted with the high mean percentage of aneuploidy observed, with 50% of the oysters analysed showing a percentage of aneuploid cells between 20% and 30%. We hypothesize that somatic aneuploidy may adversely affect oysters making them more prone to OsHV‐1 infection, but the virus is unlikely to be the cause of somatic aneuploidy.     

Grazing regime as a tool to assess positive side effects of livestock farming systems on wading birds

Wet grasslands support large populations of waders. As these birds are very sensitive to sward height and heterogeneity, grazing management is a key issue to their conservation. On a French coastal marsh consisting of 816 fields of wet grasslands, birds were monitored in spring and grazing regimes were assessed at three periods: year, spring, autumn. Each species was associated with a particular annual grazing index lower than the mean for all grazed fields. During spring, grazing intensity was significantly lower for fields occupied by birds than for those of the entire landscape. Different species of waders showed different preferences to grazing intensity with redshanks and curlews representing two extremes of a gradient going from low to high intensity. In early spring, the more precocious species selected fields with a significantly higher mean and variance in autumn stocking rate than for all grazed fields in previous autumn. These results highlight the need to maintain a variety of grazing regimes if conservation of the waders is to be achieved at the community level. On the basis of our analysis, useful indicators related to thresholds on livestock density and turn-out date can be derived to assess positive side effects of livestock farming systems.     

Constituents of the stem bark of Ormosia wayana.

The isolation of lupeol, beta-sitosterol acetate and three quinolizidinic alkaloids, (+)-lupanine, (-)-sparteine and (-)-3 beta-hydroxy-13 alpha-tigloyloxy-lupanine (1), from the stem bark of Ormosia wayana is reported.     

Spatial and temporal variability of nitrate in irrigated salad crops

The objective of this study was to analyze the spatial and seasonal variations in NO₃ ^–-N concentration in soil samples and solution samplers and the N leaching of an irrigated crop cultivated intensively in the Mediterranean zone. Although much information is available from controlled field experiments concerning N concentration and its spatial variability, quantitative estimates of nitrate fluxes under normal farming conditions and when the field is directly managed by farmers are rare. This is particularly true for gardening crops in the Mediterranean zone, where high evapotranspiration rates lead to intensive irrigation and may be responsible for N leaching. A field experiment was conducted in the Departement du Gard under agricultural conditions. Salads (Cichorium endivia, Lactuca sativa) were planted in three consecutive periods. The field was irrigated with sprinklers. Local measurements with a neutron probe were made at two sites (row, interrow), and an experimental plot (95 m×25 m) was surveyed at 36 points located on a 10 m×10 m equilateral grid to analyze the spatial variability of water and NO₃ ^–-N balances. To analyze the basic statistical properties of our sampling scheme, random fields of soil concentration were simulated with the turning-bands method. Sampling strategy simulations indicated that when a spatial structure exists, sampling according to a regular grid was more efficient than a purely random sampling strategy. Global trends indicated high spatial variability for nitrate leaching with differences between periods of different irrigation intensity (97 kg ha^–1 NO₃ ^–-N leaching during the spring and summer, and 199 kg ha^–1 NO₃ ^–-N leaching during autumn and winter). Leaching caused temporal variations in the spatial distributions of NO₃ ^–-N. The origin of the spatial variability of N leaching was explained by first, the variability in NO₃ ^–-N concentration in the soil profile, and second, by spatial variability in irrigation. Furthermore, the spatial distribution of the NO₃ ^–-N concentration was time dependent, and NO₃ ^–-N spatial distributions became independent after approximately 2 or 3 months under our conditions. Our results show that better management of irrigation and fertilizer in spring and summer may reduce N leaching and, thus, improve ground water quality. Received: 15 March 1996     

On reliability in irrigation service preliminary concepts and application

Without doubt the performance indicator that has so far received least attention in irrigation is the reliability of irrigation service. A review of reliability approaches as reflected in the literature is made and the analysis leads to propose a new conceptual framework for reliability of irrigation.The reliability of irrigation service is defined as the degree to which the irrigation system, and its water deliveries, conform to the prior expectations of its users. The perception of the user is central to the process of defining expectations and to the process of making strategic and tactical choices for the cropping pattern, the quantity of inputs, etc.It is proposed here to use a composite reliability approach, combining two key aspects: the variability and the predictability of the service characteristics. The methodology consists firstly of defining a set of three, non-overlapping, first-order indicators which fully characterize irrigation deliveries. These indicators are: Adequacy, Timeliness and Steadiness. Then the variation (in time or in space) of these indicators leads to Second-order indicators of performance. One second-order indicator is the well-known Equity, which assesses the spatial distribution or the distribution between shareholders.Variability and predictability are the two main aspects of the proposed concept of reliability. The variability is the temporal variation of the first-order indicators while the predictability defines the extent to which irrigation can be forecast. Low variability means high predictability, whereas high variability does not necessarily mean low predictability, as patterns of variation can possibly be deduced from past events.The reliability is inversely proportional to the frequency and the magnitude of failure. Here the magnitude of failure in irrigation service is measured by the deviation of the actual from the expected delivery.Existing approaches and the proposed conceptual framework are applied to a case study in the Punjab-Pakistan. It shows that reliability indicators proposed so far are not doing any better than the classical approach of adequacy. The new proposed approach for reliability, based on the combination of variability and predictability, seems more promising.Finally this preliminary analysis also identifies several key domains for which further investigations should be undertaken to increase the general understanding of reliability.     

Nitrous oxide production by nitrification and denitrification in soil aggregates as affected by O2 concentration

Nitrous oxide emitted by soils can be produced either by denitrification in anoxic conditions or by nitrification in presence of O₂. The relative importance of the two processes, particularly under varied partial pressures of O₂, is not always known. This paper focuses on the influence of O₂ concentration on N₂O production by nitrification and denitrification in an arable Orthic Luvisol. Soil aggregates (2-3 mm size), water unsaturated, received 116 mg N kg⁻¹ as ammonium sulphate labelled with ¹⁵N and were incubated during 14 days at different O₂ partial pressures: 0, 0.35, 0.76, 1.5, 4.3 and 20.4 kPa. A ¹⁵N tracing technique was used to quantify nitrification and denitrification rates. ¹⁵N₂O and ¹⁵N₂ were measured. Oxygen pressure appeared to strongly influence both nitrification and denitrification rates and also N₂O emissions. Nitrification rates were reduced by a factor of 6-9 when O₂ decreased from 20.4 to 0.35 kPa. They were highly correlated with O₂ consumption rates. Denitrification mainly occurred in complete anoxic conditions. The proportion of N₂O emitted by denitrification was estimated by two independent methods: one based on ¹⁵N tracing using isotope composition of NH₄, NO₃ and N₂O, the other based on the measurement of the ¹⁵N₂O:¹⁵N₂ ratio. The two methods gave close results. The highest N₂O emissions were obtained under complete anoxic conditions and were due to denitrification. However, N₂O emissions almost as important were obtained at day 14 with 1.5 kPa O₂ pressure, and they were due to nitrification. Nitrification was the main source of N₂O at O₂ concentrations greater than 0.35 kPa. The amounts of N₂O-N emitted by nitrification were linearly related to the amounts of N nitrified, but the slope of the regression was highly dependent on O₂ concentration: it varied from 0.16 to 1.48% when O₂ concentration was reduced from 20.4 to 0.76 kPa. Emissions of N₂O by nitrification may then be quite significant if nitrification occurs at a reduced O₂ concentration.