A rapid diagnostic assay for detection and quantification of the causal agent of strawberry wilt from field samples

Verticillium dahliae Kleb, the cause of Verticillium wilt disease, is a destructive pathogen that leads to severe yield losses in strawberry fields and thus considerable economic damages. Although rapid identification and detection methods are becoming available more, pathogen quantification remains one of the main challenges in the disease management. In this study, a real-time polymerase chain reaction (rtPCR) assay was developed to quantitatively assess V. dahliae abundance directly from affected roots and soil collected from different areas in Estonia. A specific primer pair based on the ribosomal DNA (rDNA) internally transcribed spacer was designed for SYBR Green-based assay. Strawberry plant and soil samples were randomly collected from different areas in Estonia and analyzed for V. dahliae by soil plating technique and rtPCR assay. The assay was specific for V. dahliae so that the minimum detection limit was 0.93?pg?µl^?1 of pathogen DNA and the lowest amount of V. dahliae detected in soil was 10.48?pg?µl^?1 of target DNA corresponding to one microsclerotia per gram of soil. This technique allowed rapid detection and quantification of the pathogen DNA at the picogram level in soils and even in symptomless plants, facilitating the screening of the pathogen in diverse areas. This is the first study about the rtPCR technique being used successfully to assess populations of V. dahliae with high specificity and sensitivity in Estonia strawberry fields. Results of this research can be useful for growers and agricultural organizations to improve available disease management strategies against Verticillium wilt.     

Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing

Soil fungal pathogens are the most common cause of diseases in commercial strawberry crops worldwide. Since simultaneous infections by different pathogens can severely damage the crop, understanding the associated fungal communities can be helpful to mitigate crop loss. Herein, we used Illumina metabarcoding to assess the structure of fungal communities in five strawberry production areas in Estonia. Our analysis revealed 990 to 1430 operational taxonomic units (OTUs) per soil sample (pools of eight soil samples per production area). Based on our analyses, Ascomycota (55.5%) and Basidiomycota (25.0%) were the most OTUs-rich. Amongst the 24 most abundant OTUs, Geomyces, Rhodotorula, Verticillium and Microdochium were the most abundant genera, which were found across nearly all the soil samples. The OTUs were also clustered into three distinct groups, corresponding to different functional guilds of fungi. In addition, Fusarium solani, V. dahliae, Rhizoctonia solani and Colletotrichum truncatum were enormously abundant in the fields with disease symptoms, whereas arbuscular mycorrhizal fungi especially Rhizophagus irregularis were considerably more abundant in the fields with healthy plants. These findings provide support that mycorrhizal fungi may play an important role in suppressing pathogens. Our study for the first time shows the usefulness of Illumina technology in surveying the communities of soil fungi in strawberry fields effectively, which may improve available disease management strategies against strawberry diseases.     

Early blight destroys potato foliage in the northern Baltic region

In recent years, potato early blight [Alternaria solani (Ellis & G. Martin) L.R. Jones, A lternaria alternata (Fr.) Keissl.] has occurred with increasing frequency in European potato fields, including those in northern regions. In our study, early blight was evaluated during the two years 2010–2011 on potato plants in a conventional farming experiment. Both growing seasons were very favourable for early blight development and evaluation. Our study indicates that, despite chemical treatments, potato early blight is a great problem for potato growers in conventional farming systems in the North-East region in years when temperatures are higher than average. In 2011, early blight damage was particularly high on the untreated (N0P0K0) treatment plots where severity increased abruptly from an initial 2% to 91%, and killed the potato haulms within five weeks. In 2010, the most severely infected plants were also recorded on the untreated (N0P0K0) plots, where 70% of foliage was destroyed by the end of the growing season. Results showed that a more efficient chemical strategy is needed against this disease on susceptible cultivars. Breeding and growing more resistant cultivars of potato is considered the most efficient, cost effective and environmentally friendly control method for sustainable cultivation in conventional growing systems. As an increase in the frequency of warmer summers is predicted, greater problems from this pathogen are to be expected in Northern Europe.     

Large‐scale soil maps and a supplementary database for land use planning in Estonia

A soil map at the scale 1:10,000 serves as a major important document for land owners and local governments, which allows them to use soil information in their daily activity. The intensity of exploitation of soil maps will increase when the very map and its legend are supplemented, within colored and indexed polygons, with information about soil texture and reaction by layers, but also about the thickness and characterization of the epipedon, quality indices for soil assessment, classes of stoniness, and prevalent fractions of stones, erosion risk, etc. Special maps of agronomical status, with a list of proper measures for improvement of soils and their associations, should form a regular component of large‐scale mapping. As decrease in arable land and increase in the forest area are common trends in land use, these maps and general soil data should serve as the fundamental source of information for decision making concerning land use. Data indicating the suitability of any soil for any crop should be entered in a database. Application of GIS on any level of national economy, digitization of a large‐scale soil database and making it accessible to land users would allow to expand the amount of available information for each soil map polygon.     

Elemental and Base Anions Deposition in the Snow Cover of North-Eastern Estonia

Snow samples from 18 sites in Estonia were collected in February and March 1996 after 72–110 days of permanent snow cover. Three snow layers corresponding to different snow accumulation periods were separated in each sampling site. Snow water samples were analysed for sulphate (SO₄ ^2-), nitrate (NO₃ ^-), and chloride (Cl^-) ions and elemental composition. Deposition fluxes of 27 chemical species were used for factor, cluster and correlation analysis. The effects of cement dust, oil shale fly ash, sulphur dioxide and chlorine from emissions of thermal power plants were distinguished. A large number of trace metals are strongly correlated with each other (R > 0.8) and with macro-components (except NO₃ ^-), which refers to a common origin, identified as the mineral part of oil shale. Deposition fluxes of Ca, Mg, SO₄ ^2- and a number of mineral components exceed near the power plants 1–2 decimal orders the background value. The deposition fluxes in forested sites are up to 2 times higher than in open land sites. This difference may be caused by more efficient turbulent transfer over rougher surface. It is suggested, that NO₃ ^- and Zn originate mainly and Pb, Cd and Cu partially from non-local or diffuse sources (traffic, domestic heating, far transport). The results of this research could be used to evaluate the air pollution deposition models and for ecological impact estimations.