scholarly journals Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1070
Author(s):  
Anna Czubatka-Bieńkowska ◽  
Joanna Kaczmarek ◽  
Katarzyna Marzec-Schmidt ◽  
Anna Nieróbca ◽  
Agnieszka Czajka ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Plasmodiophora Brassicae ◽  
Regional Scale ◽  
Preventative Measures ◽  
Gene Copies ◽  
Weight Method ◽  
Provinces Of Poland ◽  
Risk Potential ◽  
Inverse Distance ◽  
Vegetable Brassicas

Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures.

Archaeal ammonia oxidisers are abundant in acidic, coarse-textured Australian soils

Soil Research ◽  
2011 ◽  
Vol 49 (8) ◽  
pp. 715 ◽  
Author(s):  
Cathryn A. O'Sullivan ◽  
Steven A. Wakelin ◽  
Ian R. P. Fillery ◽  
Adrienne L. Gregg ◽  
Margaret M. Roper
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Soils ◽  
Amoa Gene ◽  
Banding Patterns ◽  
Soil Dna ◽  
Potential Nitrification ◽  
Gene Copies ◽  
Gradient Gel Electrophoresis ◽  
Key Driver ◽  
Ammonia Oxidising Archaea

The abundances of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soils underlying pastures in the south-west of Western Australia (WA) were investigated. Samples were collected from irrigated pastures and one unmanaged (driveway) area during December 2009. Archaeal and bacterial ammonia monooxygenase (amoA) genes were quantified using real-time PCR, and the diversity of the archaeal amoA genes was investigated using denaturing gradient gel electrophoresis (PCR-DGGE). AOA amoA gene copies outnumbered AOB in all samples. Numbers of archaeal amoA genes ranged from 4.1E+01 to 1.34E+05 gene copies/ng soil DNA. Bacterial amoA genes were below detection limits at three of the four sample sites and ranged from 8.9E+01 to 6.7E+02 gene copies/ng soil DNA at the remaining site. Potential nitrification rates (PNR) were not correlated with AOA or AOB gene abundance, but high PNR only occurred at the site with measureable numbers of AOB. The DGGE analysis revealed that the AOA community was diverse and variability in banding patterns was significantly affected by both site and depth (P < 0.05). Statistical analysis matching biological variation (AOA amoA genotypes) to environmental variables (BEST analysis) revealed that pH was the key driver of AOA community structure (ρ = 0.72; P = 0.005). Soil pH was also inversely correlated to abundance of AOA amoA genes in soil (ρ = 0.8; P = 0.003). This study has shown that AOA are important members of the nitrogen-cycling community in acidic WA pasture soils, and likely in the wider agricultural soils of WA.

scholarly journals Influence of Soil-Borne Inoculum of Plasmodiophora brassicae Measured by qPCR on Disease Severity of Clubroot-Resistant Cultivars of Winter Oilseed Rape (Brassica napus L.)

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 433
Author(s):  
Ann-Charlotte Wallenhammar ◽  
Zahra Saad Omer ◽  
Eva Edin ◽  
Anders Jonsson
Keyword(s):  
Disease Severity ◽  
Oilseed Rape ◽  
Plasmodiophora Brassicae ◽  
Severity Index ◽  
Field Trials ◽  
Substantial Variation ◽  
Winter Oilseed Rape ◽  
Brassica Napus L ◽  
Resistant Cultivars ◽  
Gene Copies

Use of resistant cultivars is considered the most effective tool in managing clubroot. Three clubroot-resistant commercial winter oilseed rape (OSR) cultivars and a susceptible ‘Cultivar mix’ were evaluated for disease severity index (DSI) and yield performance in field soils, selected for varying abundance of natural inoculum of Plasmodiophora brassicae. Seven field trials were carried out during 2017–2019 in winter OSR crops, and comparative bioassays were performed in a growth chamber. Substantial variation in clubroot infection between years was observed in the field trials. For Cultivar mix, a negative correlation (y = −252.3ln(x) + 58,897.6) was found between inoculum density and seed yield in five trials, whereas no correlation was found for the resistant cultivars. In bioassays, Cultivar mix exhibited a significantly high correlation between DSIb and number of gene copies g−1 soil (R2 = 0.72). For resistant cvs., Mentor and Alister, correlation was R2 = 0.45 and 0.58, respectively, indicating that resistance was under pressure. In field trials, DSIf of the resistant cultivars was lower (<27). The recommendation is thus to use clubroot-resistant cultivars of OSR as part of Integrated Pest Management in situations where abundance of P. brassicae DNA exceeds 1300 gene copies g−1 soil.

scholarly journals The detection of Plasmodiophora brassicae using loop-mediated isothermal DNA amplification

2014 ◽  
Vol 67 (4) ◽  
pp. 59-66 ◽  
Author(s):  
Joanna Kaczmarek ◽  
Witold Irzykowski ◽  
Adam Burzyński ◽  
Małgorzata Jędryczka
Keyword(s):  
Oilseed Rape ◽  
Visual Detection ◽  
Plasmodiophora Brassicae ◽  
Detection System ◽  
Screening Method ◽  
Dna Amplification ◽  
Good Alternative ◽  
Strand Displacement ◽  
Ctab Method ◽  
Vegetable Brassicas

<em>Plasmodiophora brassicae</em>, the cause of clubroot, is a very serious problem preventing from successful and profitable cultivation of oilseed rape in Poland. The pathogen was found in all main growing areas of oilseed rape; it also causes considerable problems in growing of vegetable brassicas. The aim of this work was to elaborate fast, cheap and reliable screening method to detect <em>P. brassicae</em>. To achieve this aim the Loop-mediated isothermal DNA amplification (LAMP) technique has been elaborated. The set of three primer pairs was designed using LAMP software. The detection was performed with the GspSSD polymerase, isolated from bacteria <em>Geobacillus</em> sp., with strand displacement activity. DNA extraction from clubbed roots obtained from farmers’ fields of oilseed rape infected by <em>P. brassicae</em> was done using a modified CTAB method. The reaction was performed for 60 min at 62<sup>o</sup>C. The visual detection was done using CFX96 Real Time PCR Detection System (BioRad) or Gerie II Amplicatior (Optigen). The detection with LAMP proved its usefulness; it was easy, fast and accurate and independent of plant age. The detection limit was 5 spores per 1 µl of the spore suspension, so LAMP was less sensitive than quantitative PCR tests reported in the literature. However, the method is cheap and simple, so it is a good alternative, when it comes to practical use and the assessment of numerous samples.

scholarly journals Infestation of Polish Agricultural Soils by Plasmodiophora Brassicae Along The Polish-Ukrainian Border

2014 ◽  
Vol 54 (3) ◽  
pp. 238-241 ◽  
Author(s):  
Małgorzata Jędryczka ◽  
Idalia Kasprzyk ◽  
Marek Korbas ◽  
Ewa Jajor ◽  
Joanna Kaczmarek
Keyword(s):  
Oilseed Rape ◽  
Irrigation Water ◽  
Rural Areas ◽  
Molecular Detection ◽  
Agricultural Soils ◽  
Plasmodiophora Brassicae ◽  
Soil Samples ◽  
Soil Particles ◽  
Bait Plants ◽  
Polish Variety

Abstract There has been a rapid, worldwide increase in oilseed rape production that has resulted in enormous intensification of oilseed rape cultivation, leading to tight rotations. This in turn, has caused an accumulation of pests as well as foliar and soil-borne diseases. Recently, clubroot has become one of the biggest concerns of oilseed rape growers. Clubroot is caused by the soil-borne protist Plasmodiophora brassicae Woronin. The pathogen may be present in groundwater, lakes, and irrigation water used in sprinkling systems. It can be easily transmitted from one field to another not only by water, but also by soil particles and dust transmitted by wind and on machinery. The aim of our overall study was to check for P. brassicae infestation of Polish agricultural soils. This paper presents the 2012 results of a study performed along the Polish-Ukrainian border in two provinces: Lublin (Lubelskie Voivodeship) and the Carpathian Foothills (Podkarpackie Voivodeship), in south-east Poland. Monitoring was done in 11 counties, including nine rural and two municipal ones. In total, 40 samples were collected, out of which 36 were collected from fields located in rural areas and four from municipal areas, with two per municipal region. Each sample was collected at 8-10 sites per field, using a soil auger. The biotest to detect the presence of P. brassicae was done under greenhouse conditions using seedlings of the susceptible Brassicas: B. rapa ssp. pekinensis and the Polish variety of oilseed rape B. napus cv. Monolit. Susceptible plants grown in heavily infested soils produced galls on their roots. A county was regarded as free from the pathogen, if none of the bait plants became infected. The pathogen was found in three out of 40 fields monitored (7.5%) in the Carpathian Foothill region. The fields were located in two rural counties. The pathogen was not found in Lublin province, and was also not detected in any of the municipal counties. The detection with a biotest was fully confirmed by PCR-based molecular detection of P. brassicae DNA in soil samples.

Mapping the Spatial Variability of Soil Properties: A Comparative Study of Spatial Interpolation Methods in Northeast China

2014 ◽  
Vol 535 ◽  
pp. 483-488 ◽  
Author(s):  
Xiao Yan Li ◽  
Hong Li ◽  
Hui Jia Liu
Keyword(s):  
Soil Properties ◽  
Human Activity ◽  
Ordinary Kriging ◽  
Northeast China ◽  
Prediction Methods ◽  
Regression Kriging ◽  
Hybrid Techniques ◽  
Soil Variables ◽  
Weight Method ◽  
Inverse Distance

We analyzed the variance characteristics of soil organic matter (SOM), total nitrogen (TN), extractable phosphorus (EP), and extractable potassium (EK), in Jiutai County, Northeast China, and compared different prediction methods for mapping of these four soil variables. The prediction methods used were geostatistical interpolation (ordinary kriging), inverse distance weight method, and the hybrid techniques (regression-kriging). A modified jackknifing method involving 40% partitions was used to examine the stability of validate the indices. Root mean square error (RMSE) was used as validation index, and mean RMSE was used to judge the prediction quality. The results showed that the hybrid interpolation regression-kriging cant be used in the region influenced by frequent and high-intensity human activity when the relationship between soil properties and environment factors were not obvious. The ordinary kriging was found to be the best method to fit the experimental semivariogram of SOM and EK. The inverse distance weight method fit well to predict the distribution of TN and EP. For SOM and EK, results showed that data values in the western part were higher than those in the eastern part. However, for TN and EP, there is no clear trend. Water and tillage erosion caused by human activity has weakened the structural influence and elevation and slope played key roles in the distribution of soil variables in the local area.

Comparison of Quantitative Precipitation Estimation Using Spatial Interpolation methods in Bukhan River Basin

2020 ◽  
Author(s):  
Sanghoo Yoon ◽  
Junseok Kim ◽  
Taeyong Kwon
Keyword(s):  
Spatial Interpolation ◽  
Mean Squared Error ◽  
Additive Model ◽  
Absolute Error ◽  
Interpolation Methods ◽  
Quantitative Precipitation Estimation ◽  
Precipitation Estimation ◽  
Weight Method ◽  
Inverse Distance ◽  
Spatial Interpolation Methods

&lt;p&gt;Quantitative precipitation estimation is needed to reduce damages from weather disasters such as torrential rain. This study is dealt with estimates of the quantitative precipitation using multiple spatial interpolation methods and compares the results. Inverse distance weight method and k-nearest neighborhood algorithm were considered as a deterministic approach and the general additive model and kriging methods were used as a stochastic approach. To evaluate the prediction performance, leave-one-out cross-validation was performed with the root mean squared error (RMSE), mean absolute error (MAE), bias, and correlation coefficient. The research data were rain gauged and radar data in the Bukhan river, which were collected from May 2018 to August 2019. The results showed that the inverse distance weight method reflected the spatial rainfall characteristics well. However, caution is needed because the best models vary depending on the pattern of rainfall in the sense of RMSE.&lt;/p&gt;&lt;p&gt;*This work was supported by KOREA HYDRO &amp; NUCLEAR POWER CO., LTD(No. 2018-Tech-20)&lt;/p&gt;

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