Real-time NASBA for Detection of Strawberry Vein Banding Virus

An assay for the detection of Strawberry vein banding virus (SVBV) in Fragaria spp. based on nucleic acid sequence based amplification (NASBA) and real-time detection using molecular beacons (real-time NASBA) is described. This assay was compared both with biological indexing, the current method for certification of SVBV, and a newly optimised PCR-based detection method. Performance of the assay was tested on three SVBV isolates in Fragaria indicator plants and 317 field strawberries from five European countries. The assay was shown to be SVBV-specific, testing negative for other common aphid-borne strawberry viruses. The virus was detected in purified total RNA preparations diluted a millionfold, which is an amount equivalent to 1ng of fresh material. The real-time NASBA method developed here offers the potential of a fast, sensitive and reliable approach for the routine diagnosis of strawberry stock material.     

A Natural Population of Recombinant Plum Pox Virus is Viable and Competitive under Field Conditions

The isolate BOR-3, collected in Slovakia in 1996, was recently identified as a natural recombinant between an M and D type of Plum pox virus (PPV). Biological assays demonstrated its capacity to be aphid- and graft-transmitted to various Prunus spp. hosts. A study was carried out to determine the further presence of PPV recombinants in two epidemiologically distinct areas – Slovakia and France. Tools based on PPV-M and D subgroup typing, targeting P3–6K₁, CI and CP regions of the PPV genome were used for recombinant identification. Closely related recombinant variants were detected in different Prunus spp. during a survey conducted in Slovakia in 2001, but not within a set of selected PPV isolates from France collected between 1985 and 2001. Sequence analysis of the (Cter)NIb–(Nter)CP region of 10 recombinant isolates from Slovakia showed their high homology, reaching more than 98%. All the recombinant isolates shared the same recombination breakpoint situated in the C terminus of the NIb gene. Our study demonstrates that the PPV recombinants are viable and competitive with conventional PPV-M and D isolates. The present work indicates that the occurrence of recombinants within PPV isolates might be more common than previously assumed.     

Position of the head is not associated with changes in horse vision

It has become accepted that the horse cannot see directly in front when the nose is lowered and must therefore rely on the rider. We tested the hypothesis that this conclusion would be correct only if the horse did not adjust the eyeball horizontal axis to changes of the head position. The results of the present study suggest that it is unlikely that horses have limited vision in relation to their head position when driven by the rider, and that the horse maintains the optimal horizontal eyeball position regardless of head position relative to the ground.     

Comparison of numerical, analytical, and empirical models to estimate wetting patterns for surface and subsurface drip irrigation

Due to increasing competition for water resources by urban, industrial, and agricultural users, the proportion of agricultural water use is gradually decreasing. To maintain or increase agricultural production, new irrigation systems, such as surface or subsurface drip irrigation systems, will need to provide higher water use efficiency than those traditionally used. Several models have been developed to predict the dimensions of wetting patterns, which are important to design optimal drip irrigation system, using variables such as the emitter discharge, the volume of applied water, and the soil hydraulic properties. In this work, we evaluated the accuracy of several approaches used to estimate wetting zone dimensions by comparing their predictions with field and laboratory data, including the numerical HYDRUS-2D model, the analytical WetUp software, and selected empirical models. The soil hydraulic parameters for the HYDRUS-2D simulations were estimated using either Rosetta for the laboratory experiments and inverse analysis for the field experiments. The mean absolute error (MAE) was used to compare the model predictions and observations of wetting zone dimensions. MAE for different experiments and directions varied from 0.87 to 10.43 cm for HYDRUS-2D, from 1 to 58.1 cm for WetUp, and from 1.34 to 12.24 cm for other empirical models.     

Pathogenic profile and cytotoxic activity of Aeromonas spp. isolated from Pectinatella magnifica and surrounding water in the South Bohemian aquaculture region

Pectinatella magnifica is an invasive freshwater bryozoan that has expanded in many localities worldwide, including fishing areas. It contains microbial communities, predominantly consisting of Aeromonas bacteria that are frequently associated with fish infections. The objective of this study was to investigate the potential pathogenicity of Aeromonas spp. associated with P. magnifica and evaluate the health risks for fish. Aeromonas strains were isolated from P. magnifica (101 strains) and from surrounding water (29 strains) in the South Bohemian region and investigated for the presence of 14 virulence-associated genes using PCR. We demonstrated high prevalence of phospholipase GCAT, polar flagellin, enolase, DNAse, aerolysin/cytotoxic enterotoxin, serine protease and heat-stable cytotonic enterotoxin-coding genes. Further, all twelve isolates that were analysed for cytotoxicity against intestinal epithelial cells were found to be cytotoxic. Six of the isolates were also tested as co-cultures composed of pairs. Enhanced cytotoxicity was observed when the pair was composed of strains from different species. In conclusion, P. magnifica is colonized by Aeromonas strains that have a relatively high prevalence of virulence-associated genes and the ability to provoke disease. Results also suggest a possibly increased risk arising from mixed infections.     

Multilocus sequence typing reveals the presence of three distinct flavescence dorée phytoplasma genetic clusters in Croatian vineyards

Flavescence dorée phytoplasma (FDp) is a quarantine pathogen associated with a severe and epidemic grapevine yellows disease representing a great threat for grapevine cultivation in Europe. An increase in disease spread prompted efforts to identify FDp strains in Croatia. Over 800 samples of grapevine together with presumed reservoir plants and almost 400 samples of Scaphoideus titanus and other potential vectors were collected countrywide and analysed. FDp isolates were characterized by multilocus sequence typing (MLST) of map, secY and uvrB-degV genes in order to determine genetic diversity and structure of FDp populations, and to trace transmission pathways. FD-related phytoplasmas were found in Croatia for the first time in alder, the invasive tree species Ailanthus altissima and leafhopper Phlogotettix cyclops. Phylogenetic analysis revealed the presence of three mapFD strain clusters: mapFD1, mapFD2 and mapFD3, and for the first time in Croatia a case of Palatinate grapevine yellows strain A (PGY-A). In total, 7 different map, 10 secY and 11 uvrB-degV genotypes were detected. The identification of 15 comprehensive FDp genotypes based on MLST suggests separate routes for disease introduction and propagation origins in Croatia. Moreover, high genetic variability of Croatian isolates indicates a complex ecological cycle of FDp involving various hosts.     

Effect of soil CO2 concentration on microbial biomass

The effect of increasing soil CO₂ concentration was studied in six different soils. The soils were incubated in ambient air (0.05 vol.% CO₂) or in air enriched with CO₂ (up to 5.0 vol.% CO₂). Carbon dioxide evolution, microbial biomass, growth or death rate quotients and glucose decay rate were measured at 6, 12 and 24 h of CO₂ exposure. The decrease in soil respiration ranged from 7% to 78% and was followed by a decrease in microbial biomass by 10–60% in most cases. High CO₂ treatments did not affect glucose decay rate but the portion of C_gluc mineralized to CO₂ was lowered and a larger portion of C_gluc remained in soils. This carbon was not utilized by soil microorganisms. Received: 30 August 1996     

Complete or incomplete dominance of resistance of the oat cultivar Delphin as a function of crown rust culture

Summary In oat cv. Delphin (Bonda x Carstens Vii) two complementary genes were found conferring resistance to sixteen cultures of ten crown rust (Puccinia coronata Cda. var. avenae Fraser ET Led.) races. The complementary genes showed full dominance to eight races and incomplete dominance to two races.     

Properties and bioavailability of particulate and mineral‐associated organic matter in Arctic permafrost soils,Lower Kolyma Region,Russia

Permafrost degradation may cause strong feedbacks of arctic ecosystems to global warming, but this will depend on if, and to what extent, organic matter (OM) is protected against biodegradation by mechanisms other than freezing and anoxia. Here, we report on the amount, chemical composition and bioavailability of particulate (POM) and mineral‐associated OM (MOM) in permafrost soils of the East Siberian Arctic. The average total organic carbon (OC) stock across all soils was 24.0 ± 6.7 kg m^?2 within 100 cm soil depth. Density fractionation (density cut‐off 1.6 g cm^?3) revealed that 54 ± 16% of the total soil OC and 64 ± 18% of OC in subsoil horizons was bound to minerals. As well as sorption of OM to clay‐sized minerals (R² = 0.80; P < 0.01), co‐precipitation of OM with hydrolyzable metals may also transfer carbon into the mineral‐bound fraction. Carbon:nitrogen ratios, stable carbon and nitrogen isotopes, ¹³C‐NMR and X‐ray photoelectron spectroscopy showed that OM is transformed in permafrost soils, which is a prerequisite for the formation of mineral‐organic associations. Mineral‐associated OM in deeper soil was enriched in ¹³C and ¹⁵N, and had narrow C:N and large alkyl C:(O‐/N‐alkyl C) ratios, indicating an advanced stage of decomposition. Despite being up to several thousands of years old, when incubated under favourable conditions (60% water‐holding capacity, 15°C, adequate nutrients, 90 days), only 1.5–5% of the mineral‐associated OC was released as CO₂. In the topsoils, POM had the largest mineralization but was even less bioavailable than the MOM in subsoil horizons. Our results suggest that the formation of mineral‐organic associations acts as an important additional factor in the stabilization of OM in permafrost soils. Although the majority of MOM was not prone to decomposition under favourable conditions, mineral‐organic associations host a readily accessible carbon fraction, which may actively participate in ecosystem carbon exchange.