The use of infrared spectroscopy and machine learning tools for detection of Meloidogyne infestations

Plant parasitic nematodes are generally soilborne pathogens that attack plants and cause economic losses in many crops. The infested plants show nonspecific symptoms or, often, are symptomless; therefore, diagnosis is performed by taking soil and root tissue samples. Here, we show that a combination of different infrared spectra analysis and machine learning algorithms can be used to detect plant parasitic nematode infestations before symptoms become visible, using leaves instead of roots and soil as samples. We found that tomato and guava plants infested with Meloidogyne enterorlobii produced different spectral patterns compared to uninfested plants. Using partial spectra from 1,450 to 900/cm as the "fingerprint region", principal component analyses indicated that after 5 (tomatoes) or 8 weeks (guava), plants with no visible symptoms of infestations were positively diagnosed. To improve the early detection response, we used machine learning modelling. A support vector machine (SVM) was used to obtain more robust, accurate models. The SVM model contained 34 support vectors, 17 for each level. The overall performance of the model was >97% and the total accuracy was significantly higher, demonstrating the absence of chance prediction. The best prediction of infestation was obtained at the second and fourth weeks for tomatoes and guavas, respectively, reducing the diagnostic time by half. The combined application of these techniques reduces the processing time from field to laboratory and shows enormous advantages by avoiding root and soil sampling.     

The effectiveness of consistent roguing in managing banana bunchy top disease in smallholder production in Africa

The removal of infected individuals is a common practice in the management of plant disease outbreaks. It minimizes the contact between healthy individuals and inoculum sources by reducing the infectious window of contaminated individuals. This requires early detection and consistent removal at landscape scale. Roguing of mats with symptoms of banana bunchy top disease (BBTD) in Cavendish banana production systems has been tested in Australia, using trained personnel, but has never been tested in smallholder systems. We studied the effectiveness of long-term consistent roguing in prolonging the productivity of banana orchards under smallholder farming systems in highland banana and plantain dominated production systems in Africa. We assessed the possibility of low-risk seed sourcing from the managed plots. Roguing reduced BBTD incidence to 2% in managed farmer fields and to 10% in experimental field plots, while a nonmanaged field eventually collapsed in the same period. With roguing, new infections decreased monthly compared to an exponential increase in a nonmanaged field. The emergence of new infections in both managed and nonmanaged farms followed a seasonal cycle. BBTD managed plots were a source of low-risk seed for replacing the rogued mats in the same fields, but perhaps not safe for use in nonendemic areas. We conclude that it is possible for smallholder farmers to recover and maintain banana productivity with rigorous roguing, which would entail early identification of symptoms and early removal of diseased mats. Studies are needed on the intensity of roguing under different disease and production conditions.     

Temporal disease dynamics and relative importance of sexual and asexual reproduction of grape downy mildew (Plasmopara viticola) in an isolated vineyard in the North Georgia Mountains,USA

The North Georgia Mountains are the southernmost region along the United States East Coast where European wine grapes (Vitis vinifera) are grown commercially. Epidemics of downy mildew, caused by Plasmopara viticola, are frequent and severe, but little is known about the epidemiology and population biology of the pathogen in this region. Disease monitoring in an experimental vineyard from 2015 to 2017 indicated that times of disease onset and progress rates were highly variable across years and cultivars. Oospores were observed microscopically, and simulation with a process-based model indicated presence of conditions favourable for oospore germination in the spring and early summer each year. A total of 409 P. viticola isolates collected over three  years were genotyped with seven microsatellite markers, revealing very high genotypic diversity, which when combined with the observation of oospores is indicative of a sexually reproducing population. Among the 409 isolates, 225 multilocus genotypes (MLGs) were identified, of which 164 were detected only once and 61 were repeated (clonal). Eight MLGs (represented by 28 isolates) were detected across years, suggesting the possibility of asexual overwintering of P. viticola in this region. Across sampling dates, the percentage of isolates belonging to nonrepeated (unique) MLGs ranged from 27.3% to 63.2%. Even towards the end of the annual epidemic, the percentage of isolates in nonrepeated MLGs was still relatively high, around 30%. These MLGs may have originated from oospores germinating late during the growing season, although incomplete sampling at earlier dates and contribution by immigration cannot be fully excluded.     

Effect of soil acidification on the growth and nitrogen use efficiency of maize in Ultisols

Purpose

To examine the effect of soil acidification on growth and nitrogen (N) uptake by maize in Ultisols.

Materials and methods

A clay Ultisol derived from Quaternary red earth and a sandy Ultisol derived from tertiary red sandstone were used in this study. A pot experiment was conducted with maize growing in the two Ultisols acidified to different pH values. Urea with ¹⁵N abundance of 10.11% was used to investigate the distribution of N fertilizer between soil and plant. Total N content and ¹⁵N abundance in plant and soil samples were determined by elemental analysis-isotope mass spectrometry.

Results and discussion

Critical soil pHs of 4.8 and 5.0 were observed for maize growing in the clay and sandy Ultisols, respectively. Below the critical soil pH, increasing soil pH significantly increased maize height and the yield of maize shoots and roots (both P < 0.05), but changes in soil pH showed no significant effect on maize growth above the critical soil pH in both Ultisols. Maize growing in the sandy Ultisol was more sensitive to changes in soil pH than in the clay Ultisol. Increase in the pH in both Ultisols also increased N accumulation in maize, the N derived from fertilizer in maize, physiological N use efficiency, and N use efficiency (NUE) by maize. Changes in soil pH had a greater effect on these parameters below the critical soil pH, compared to above. The change in soil pH had a greater effect on N accumulation in maize, the N derived from fertilizer in maize, and NUE in the sandy Ultisol than in the clay Ultisol. The NUE increased by 24.4% at pH 6.0, compared with pH 4.0 in the clay Ultisol, while the NUE at pH 5.0 was 4.8 times that at pH 4.0 in the sandy Ultisol. The increase in soil pH increased the ratio of N accumulation in maize/soil residue N and decreased the potential loss of fertilizer N from both Ultisols.

Conclusions

Soil acidification inhibited maize growth, reduced N uptake by maize, and thus, decreased NUE. To maintain soil pH of acidic soils above the critical values for crops is of practical importance for sustainable food production in acidic soils.

     

Surgical treatment of a mammary gland comedocarcinoma in an Arabian mare: Post-operative management,and histopathological and immunohistochemical features

A lactating 20-year-old, brown, Arabian mare, weighing about 300 kg, presented for bleeding from one teat and severe swelling of the entire mammary gland. The mare had untreated mastitis 10 months before. Consequently, a gangrenous teat developed after chronic bloody and purulent discharges. The teat was removed surgically by the field veterinarian. At that time, the mammary gland increased in size. Bloody and purulent discharges restarted 10 days previously. Under general anaesthesia, the entire mammary gland was removed. Comedocarcinoma was diagnosed by histopathological assessment. Immunohistochemical staining was performed for pan-cytokeratin and vimentin. Microscopic examination of immunohistochemical stained slides revealed expression of pan-cytokeratin. In conclusion, this report describes clinical, macroscopic, histopathological and immunohistochemical characteristics of comedocarcinoma that did not metastasise to regional lymph nodes. Reports in the field of equine oncology contribute to improved general knowledge in equine medicine, contributing to better diagnosis and treatment.     

Isolating the effect of soil properties on agricultural soil greenhouse gas emissions under controlled conditions

Agricultural soils are important sources of greenhouse gases (GHGs). Soil properties and environmental factors have complex interactions which influence the dynamics of these GHG fluxes. Four arable and five grassland soils which represent the range of soil textures and climatic conditions of the main agricultural areas in the UK were incubated at two different moisture contents (50 or 80% water holding capacity) and with or without inorganic fertiliser application (70 kg N ha⁻¹ ammonium nitrate) over 22 days. Emissions of N₂O, CO₂ and CH₄ were measured twice per week by headspace gas sampling, and cumulative fluxes were calculated. Multiple regression modelling was carried out to determine which factors (soil mineral N, organic carbon and total nitrogen contents, C:N ratios, clay contents and pH) that best explained the variation in GHG fluxes. Clay, mineral N and soil C contents were found to be the most important explanatory variables controlling GHG fluxes in this study. However, none of the measured variables explained a significant amount of variation in CO₂ fluxes from the arable soils. The results were generally consistent with previously published work. However, N₂O emissions from the two Scottish soils were substantially more sensitive to inorganic N fertiliser application at 80% water holding capacity than the other soils, with the N₂O emissions being up to 107 times higher than the other studied soils.     

Genetic diversity and aggressiveness of Calonectria pteridis in Eucalyptus spp.

Calonectria leaf blight, caused by Calonectria pteridis, is currently one of the main foliar diseases in eucalypt plantations in Brazil. In warm and high rainfall regions, the disease can be a limiting factor for eucalypt production when planting susceptible genotypes. The most effective method for controlling this disease in the field is the use of resistant genotypes, which requires knowledge of the genetic variability and aggressiveness of the pathogen population for effective deployment of plant resistance. This work evaluated the genetic diversity and aggressiveness of C. pteridis populations obtained from infected eucalypt plants in Monte Dourado (Pará state) and Imperatriz (Maranhão state), Brazil. To study the genetic diversity, 16 ISSR primers were tested, five of which amplified polymorphic, reproducible and informative bands. Thirty-one closely related genotypes were identified from 84 isolates studied, indicating that the population has a low genetic diversity. The aggressiveness of seven isolates, selected according to geographic origin and their clustering in the ISSR-based dendogram, was determined by inoculation of a hybrid Eucalyptus grandis × E. urophylla clone under controlled conditions. Disease severity was assessed by both measuring the percentage of plant defoliation and assigning a score according to a diagrammatic scale of symptoms. A high correlation between the two evaluation methods was observed, which revealed significant differences in aggressiveness among the isolates. The diagrammatic scale is recommended for disease evaluation because results are obtained much faster, before the occurrence of severe defoliation. No correlation between clustering in the ISSR-based phylogenetic analysis and aggressiveness was observed.     

Performance of Mixed Species and Mono‐specific Algal Diets for Culture of Larval Western School Prawns,Metapenaeus dalli

The effect of three mono‐specific and four combinations of the diatoms Chaetoceros muelleri, Chaetoceros calcitrans, and the chlorophyte Tetraselmis suecica on survival, development, and dry weight of the western school prawn, Metapenaeus dalli, was assessed from protozoea I until mysis I. The development and dry weight of larvae were significantly greater when fed diets comprising C. muelleri and/or T. suecica. A fourth diet, consisting of all three microalgal species also performed just as well. Survival alone was a poor measure of the performance of the various diets. Larvae fed with C. calcitrans, either alone or in a mixed diet with either C. muelleri or T. suecica, had significantly slower development and lower dry weight. Overall performance, assessed using the normalized biomass development index, determined that both mono‐specific and mixed diets containing C. muelleri and T. suecica were among the best for M. dalli larvae. These results for M. dalli are consistent with those found for commercially grown penaeid prawns. This study enhances the limited knowledge on the feeding requirements of metapenaeid prawn larvae. Moreover, the results will help improve hatchery methods for the aquaculture‐based enhancement of M. dalli in the Swan‐Canning Estuary and potentially increase the abundance of this iconic recreational species.     

Rhynchosporium leaf scald disease incidence: seed source and spatial pattern

A programme of field trials for the study of the winter barley–Rhynchosporium commune pathosystem is reported. The associated seedborne disease rhynchosporium leaf scald is regarded as having an important impact on barley yields. The analysis in this study relates to the impact of the seed source (commercial or farm-saved seed) on disease incidence and to the spatial pattern of rhynchosporium leaf scald disease incidence. Disease incidence data were calculated from field data recorded as disease severity. Mean disease incidence was higher in the crops grown from farm-saved seed than in those grown from commercial seed, although great agronomic significance cannot be attached to this result. The spatial pattern of rhynchosporium leaf scald disease incidence was characterized in terms of the binary power law (BPL) and was indicative of an aggregated pattern. Programme-wide BPL results were described using a novel phytopathological application of a random coefficients model. These results have application in field sampling for rhynchosporium leaf scald disease.     

Synchytrium endobioticum – risk from biogas plants?

Synchytrium endobioticum is one of the most important pathogens of potato and is known for its persistent propagation structures. Under favourable conditions, infection of highly susceptible potato cultivars leads to clearly visible cauliflower‐like tissue warts, the typical symptom of potato wart disease. However, unfavourable infection conditions or low infection pressure may result in symptoms being overlooked. Thus, the introduction of pathogen structures into stages of the processing industry cannot be ruled out. As the amounts of processed potato products continue to rise, phytosanitary risks from processing discarded potatoes and potato waste in biogas plants have to be considered. Hence, the resilience of resting spores against mesophilic anaerobic digestion was analysed in stirred tank reactors. Laboratory‐scale results show that S. endobioticum not only withstands mesophilic anaerobic digestion but also subsequent storage of the digestate for at least 4 weeks. Large numbers of viable resting spores were detectable by microscopic assessment in all samples. Viability was proved and verified additionally by bioassay. Consequently, potatoes, potato waste and processing water from potato processing industries used in biogas plants pose a phytosanitary risk if the accruing digestates are returned as fertilizer to arable land.