scholarly journals Microbiome Analysis of the Rhizosphere from Wilt Infected Pomegranate Reveals Complex Adaptations in Fusarium—A Preliminary Study

Agriculture ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 831
Author(s):  
Anupam J. Das ◽  
Renuka Ravinath ◽  
Talambedu Usha ◽  
Biligi Sampgod Rohith ◽  
Hemavathy Ekambaram ◽  
...  
Keyword(s):  
Early Stage ◽  
Soil Nutrient ◽  
Intermediate Stage ◽  
Rapid Identification ◽  
Wilt Disease ◽  
Soil Samples ◽  
Carbohydrate Binding ◽  
Microbiome Analysis ◽  
Metagenome Sequencing ◽  
Achromobacter Sp

Wilt disease affecting pomegranate crops results in rapid soil-nutrient depletion, reduced or complete loss in yield, and crop destruction. There are limited studies on the phytopathogen Fusarium oxysporum prevalence and associated genomic information with respect to Fusarium wilt in pomegranate. In this study, soil samples from the rhizosphere of different pomegranate plants showing early stage symptoms of wilt infection to an advanced stage were collected from an orchard situated in Karnataka, India. A whole metagenome sequencing approach was employed to gain insights into the adaptations of the causative pathogen F. oxysporum. Physicochemical results showed a drop in the pH levels, N, Fe, and Mn, and increase in electrical conductivity, B, Zn, Cl, Cu was observed in the early and intermediate stage samples. Comparative abundance analysis of the experimental samples ESI and ISI revealed an abundance of Proteobacteria phyla Achromobacter sp. 2789STDY5608625, Achromobacter sp. K91, and Achromobacter aegrifaciens and Eukaryota namely Aspergillus arachidicola, Aspergillus candidus, and Aspergillus campestris. Functional pathway predictions implied carbohydrate binding to be significant (p < 0.05) among the three experimental samples. Microbiological examination and whole microbiome analysis confirmed the prevalence of F. oxysporum in the soil samples. Variant analysis of F. oxysporum revealed multiple mutations in the 3IPD gene with high impact effects. 3-Isopropylmalate dehydratase and carbohydrate-active enzymes could be good targets for the development of antifungals that could aid in biocontrol of F. oxysporum. The present study demonstrates the capabilities of the whole metagenome sequencing approach for rapid identification of potential key players of wilt disease pathogenesis wherein the symptomatology is complex.

scholarly journals Early detection of pine wilt disease in Pinus tabuliformis in North China using a field portable spectrometer and UAV-based hyperspectral imagery

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Run Yu ◽  
Lili Ren ◽  
Youqing Luo
Keyword(s):  
Early Stage ◽  
Vegetation Indices ◽  
Pine Wilt Disease ◽  
Wilt Disease ◽  
Pinus Tabulaeformis ◽  
Pine Tree ◽  
Preventative Measures ◽  
Pine Wilt ◽  
Pine Trees ◽  
Airborne Vehicle

Abstract Background Pine wilt disease (PWD) is a major ecological concern in China that has caused severe damage to millions of Chinese pines (Pinus tabulaeformis). To control the spread of PWD, it is necessary to develop an effective approach to detect its presence in the early stage of infection. One potential solution is the use of Unmanned Airborne Vehicle (UAV) based hyperspectral images (HIs). UAV-based HIs have high spatial and spectral resolution and can gather data rapidly, potentially enabling the effective monitoring of large forests. Despite this, few studies examine the feasibility of HI data use in assessing the stage and severity of PWD infection in Chinese pine. Method To fill this gap, we used a Random Forest (RF) algorithm to estimate the stage of PWD infection of trees sampled using UAV-based HI data and ground-based data (data directly collected from trees in the field). We compared relative accuracy of each of these data collection methods. We built our RF model using vegetation indices (VIs), red edge parameters (REPs), moisture indices (MIs), and their combination. Results We report several key results. For ground data, the model that combined all parameters (OA: 80.17%, Kappa: 0.73) performed better than VIs (OA: 75.21%, Kappa: 0.66), REPs (OA: 79.34%, Kappa: 0.67), and MIs (OA: 74.38%, Kappa: 0.65) in predicting the PWD stage of individual pine tree infection. REPs had the highest accuracy (OA: 80.33%, Kappa: 0.58) in distinguishing trees at the early stage of PWD from healthy trees. UAV-based HI data yielded similar results: the model combined VIs, REPs and MIs (OA: 74.38%, Kappa: 0.66) exhibited the highest accuracy in estimating the PWD stage of sampled trees, and REPs performed best in distinguishing healthy trees from trees at early stage of PWD (OA: 71.67%, Kappa: 0.40). Conclusion Overall, our results confirm the validity of using HI data to identify pine trees infected with PWD in its early stage, although its accuracy must be improved before widespread use is practical. We also show UAV-based data PWD classifications are less accurate but comparable to those of ground-based data. We believe that these results can be used to improve preventative measures in the control of PWD.

scholarly journals Chest computed tomography imaging features in patients with coronavirus disease 2019 (COVID-19)

2021 ◽  
Vol 49 (5) ◽  
pp. 030006052110106
Author(s):  
Hoda Salah Darwish ◽  
Mohamed Yasser Habash ◽  
Waleed Yasser Habash
Keyword(s):  
Computed Tomography ◽  
Intermediate Phase ◽  
Early Stage ◽  
Lower Lobe ◽  
Ground Glass Opacity ◽  
Intermediate Stage ◽  
Mediastinal Lymphadenopathy ◽  
Imaging Features ◽  
Stage Disease ◽  
Bilateral Lesions

Objective To analyze computed tomography (CT) features of symptomatic patients with coronavirus disease 2019 (COVID-19). Methods Ninety-five symptomatic patients with COVID-19 confirmed by reverse-transcription polymerase chain reaction from 1 May to 14 July 2020 were retrospectively enrolled. Follow-up CT findings and their distributions were analyzed and compared from symptom onset to late-stage disease. Results Among all patients, 15.8% had unilateral lung disease and 84.2% had bilateral disease with slight right lower lobe predilection (47.4%). Regarding lesion density, 49.4% of patients had pure ground glass opacity (GGO) and 50.5% had GGO with consolidation. Typical early-stage patterns were bilateral lesions in 73.6% of patients, diffuse lesions (41.0%), and GGO (65.2%). Pleural effusion occurred in 13.6% and mediastinal lymphadenopathy in 11.5%. During intermediate-stage disease, 47.4% of patients showed GGO as the disease progressed; however, consolidation was the predominant finding (52.6%). Conclusion COVID-19 pneumonia manifested on lung CT scans with bilateral, peripheral, and right lower lobe predominance and was characterized by diffuse bilateral GGO progressing to or coexisting with consolidation within 1 to 3 weeks. The most frequent CT lesion in the early, intermediate, and late phases was GGO. Consolidation appeared in the intermediate phase and gradually increased, ending with reticular and lung fibrosis-like patterns.

Reproductive Failure in Populations of the Dog-Whelk, Nucella Lapillus, Caused by Imposex Induced by Tributyltin from Antifouling Paints

1986 ◽  
Vol 66 (4) ◽  
pp. 767-777 ◽  
Author(s):  
P. E. Gibbs ◽  
G. W. Bryan
Keyword(s):  
Vas Deferens ◽  
Early Stage ◽  
Premature Death ◽  
Intermediate Stage ◽  
Reproductive Failure ◽  
Nucella Lapillus ◽  
Egg Capsules ◽  
Male Characters ◽  
High Incidence ◽  
Declining Populations

The development of male characters, notably a penis and a vas deferens, on the female (the phenomenon of ‘imposex’) of the dog-whelk, Nucella lapillus, is described. Three stages are recognized: an ‘early’ stage involving the formation of a vas deferens and a small penis, an ‘intermediate’ stage characterized by the enlargement of the female penis to a size approaching that of the male and a ‘late’ stage during which the female opening (vulva) is occluded by overgrowth of vas deferens tissue. This blockage of the pallial oviduct prevents the release of egg capsules and renders the female sterile. The extent and cause of such reproductive failure is evident from the high incidence of females containing aborted capsules in declining populations close to sources of tributyltin (TBT) contamination. These same populations comprise fewer females than expected and it would appear that the accumulation of aborted capsules within the pallial oviduct eventually causes the premature death of the female.

scholarly journals Quantification of Hydrocarbon Abundance in Soils Using Deep Learning with Dropout and Hyperspectral Data

2019 ◽  
Vol 11 (16) ◽  
pp. 1938 ◽  
Author(s):  
Asmau M. Ahmed ◽  
Olga Duran ◽  
Yahya Zweiri ◽  
Mike Smith
Keyword(s):  
Deep Learning ◽  
Contaminated Soils ◽  
Early Stage ◽  
Imaging Techniques ◽  
Rapid Identification ◽  
Hyperspectral Data ◽  
Learning Approach ◽  
Backpropagation Algorithm ◽  
Average Mean Square Error ◽  
Deep Learning Neural Network

Terrestrial hydrocarbon spills have the potential to cause significant soil degradation across large areas. Identification and remedial measures taken at an early stage are therefore important. Reflectance spectroscopy is a rapid remote sensing method that has proven capable of characterizing hydrocarbon-contaminated soils. In this paper, we develop a deep learning approach to estimate the amount of Hydrocarbon (HC) mixed with different soil samples using a three-term backpropagation algorithm with dropout. The dropout was used to avoid overfitting and reduce computational complexity. A Hyspex SWIR 384 m camera measured the reflectance of the samples obtained by mixing and homogenizing four different soil types with four different HC substances, respectively. The datasets were fed into the proposed deep learning neural network to quantify the amount of HCs in each dataset. Individual validation of all the dataset shows excellent prediction estimation of the HC content with an average mean square error of ~ 2 . 2 × 10 - 4 . The results with remote sensed data captured by an airborne system validate the approach. This demonstrates that a deep learning approach coupled with hyperspectral imaging techniques can be used for rapid identification and estimation of HCs in soils, which could be useful in estimating the quantity of HC spills at an early stage.

scholarly journals The role of bacteria in pine wilt disease: insights from microbiome analysis

2018 ◽  
Vol 94 (7) ◽  
Author(s):  
Marta Alves ◽  
Anabela Pereira ◽  
Cláudia Vicente ◽  
Patrícia Matos ◽  
Joana Henriques ◽  
...  
Keyword(s):  
Pine Wilt Disease ◽  
Wilt Disease ◽  
Microbiome Analysis ◽  
Pine Wilt

Effect of lignite humic acid on soil nutrient availability at different growth stages of rice grown on Vertisols and Alfisols

2004 ◽  
Vol 52 (3) ◽  
pp. 227-235 ◽  
Author(s):  
R. Nandakumar ◽  
A. Saravanan ◽  
P. Singaram ◽  
B. Chandrasekaran
Keyword(s):  
Humic Acid ◽  
Nutrient Availability ◽  
Field Experiments ◽  
Soil Nutrient ◽  
Soil Samples ◽  
Growth Stages ◽  
Research Station ◽  
Soil Nutrient Availability ◽  
Npk Fertilizers ◽  
Soil Application

Field experiments were conducted with rice (ADT-39) during the wet Kharif season (July- October 2001) at two locations, the Tamil Nadu Rice Research Institute (TRRI) farm, Aduthurai (Vertisol) and the Agricultural Research Station (ARS) farm, Pattukkottai (Alfisol), representing the old and new delta areas of the Cauvery, respectively. The same set of treatments was followed in both soils. The treatments consisted of the recommended NPK fertilizer application at 75% and 100% alone, and 10 or 20 kg ha-1 humic acid (HA) in combination with NPK fertilizers as soil application, besides an integrated method involving soil application, root dipping and foliar spraying with humic acid and NPK fertilizers. initial soil samples from the experimental fields were analysed for physical, physico-chemical and chemical properties. Surface soil samples were collected at critical growth stages and analysed for various available nutrients. The results of the field experiments revealed that the application of humic acid along with inorganic fertilizers led to higher soil nutrient availability at all the growth stages of rice. Similar results were obtained in both Vertisol and Alfisol. The present investigation concluded that the best treatment for soil nutrient availability was 10 kg ha-1 HA (soil application) + 0.1% HA foliar spray (twice) + 0.3% HA root dipping + 100% NPK, which was on par with the treatment involving 20 kg ha-1 HA (soil application) + 100% NPK compared to the other treatments.

scholarly journals Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 91 ◽  
Author(s):  
Akiko Ogawa ◽  
Keito Takakura ◽  
Katsuhiko Sano ◽  
Hideyuki Kanematsu ◽  
Takehiko Yamano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Silver Nanoparticle ◽  
Biofilm Formation ◽  
Early Stage ◽  
Biofilm Reactor ◽  
Next Generation ◽  
Microbiome Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Closed Laboratory

Previously, we demonstrated that silver nanoparticle-dispersed silane-based coating could inhibit biofilm formation in conditions where seawater was used as a bacterial source and circulated in a closed laboratory biofilm reactor. However, it is still unclear whether the microbiome of a biofilm of silver nanoparticle-dispersed silane-based coating samples (Ag) differs from that of a biofilm of non-dispersed silane-based coating samples (Non-Ag). This study aimed to perform a microbiome analysis of the biofilms grown on the aforementioned coatings using a next-generation sequencing (NGS) technique. For this, a biofilm formation test was conducted by allowing seawater to flow through a closed laboratory biofilm reactor; subsequently, DNAs extracted from the biofilms of Ag and Non-Ag were used to prepare 16S rRNA amplicon libraries to analyze the microbiomes by NGS. Results of the operational taxonomy unit indicated that the biofilms of Non-Ag and Ag comprised one and no phyla of archaea, respectively, whereas Proteobacteria was the dominant phylum for both biofilms. Additionally, in both biofilms, Non-Ag and Ag, Marinomonas was the primary bacterial group involved in early stage biofilm formation, whereas Anaerospora was primarily involved in late-stage biofilm formation. These results indicate that silver nanoparticles will be unrelated to the bacterial composition of biofilms on the surface of silane-based coatings, while they control biofilm formation there.

scholarly journals Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis

2019 ◽  
Vol 10 ◽  
Author(s):  
Joana Pereira-Marques ◽  
Anne Hout ◽  
Rui M. Ferreira ◽  
Michiel Weber ◽  
Ines Pinto-Ribeiro ◽  
...  
Keyword(s):  
Sequencing Depth ◽  
Taxonomic Resolution ◽  
Microbiome Analysis ◽  
Metagenome Sequencing

Transition phenomena in diffusive motions due to the change of memory effects

2019 ◽  
Vol 34 (01) ◽  
pp. 2050013
Author(s):  
Dongmi Kim ◽  
Hyun-Joo Kim
Keyword(s):  
Stochastic Process ◽  
Memory Effect ◽  
Stochastic Models ◽  
Hurst Exponent ◽  
Early Stage ◽  
Intermediate Stage ◽  
Memory Effects ◽  
Replication Process ◽  
Normal Diffusion ◽  
Previous Step

In the anomalous diffusions, the transition phenomena from superdiffusion (or subdiffusion) to normal diffusion have been found in several experiments and studied by stochastic models. In this study, we found the diffusion transition which occurs twice in a stochastic process, first from superdiffusion to subdiffusion, and then from subdiffusion to normal diffusion by using the nonstationary Markovian replication process with the memory of the previous step exponentially decaying with time. In the early stage, when the walker strongly follows the previous step, superdiffusive behaviors occur, while in the intermediate stage in which the memory effect decays exponentially, the motion of the walker shows subdiffusive behaviors. Eventually, as the memory effect almost disappears, the motion reduces to normal diffusion. We also found that the Hurst exponent in the intermediate subdiffusive region becomes smaller when the change of the memory effect is more abrupt.

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