Leaf rot caused by Rhizopus oryzae on pak choy (Brassica campestris ssp. chinensis) in China

Pak choy (Brassica campestris ssp. chinensis L.) is the major vegetable crop cultivated in China. During December 2017, leaf rot was frequently observed on leaves of pak choy in greenhouses of Shanghai, China. Diseased leaf samples were plated onto acidified potato dextrose agar and fungal cultures were isolated and identified as Rhizopus oryzae, based on morphological features and molecular identification. Definitive identification as R. oryzae was based on the comparative molecular analysis of rRNA gene sequences. Blast analysis revealed 99% similarity with R. oryzae. Pathogenicity was determined by inoculating healthy pak choy leaves and plants with hyphal suspensions of R. oryzae. The fungus was re-isolated from developing similar lesions on the inoculated plants and identified as similar to the inoculated fungus, thus fulfilling Koch’s postulates. This is the first report of fungal leaf rot caused by R. oryzae on pak choy in China

PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba

Evaluation of Metal Tolerance of Fungal Strains Isolated from Contaminated Mining Soil of Nanjing, China

Simple Summary In this study, cadmium, chromium, and lead tolerant microbes have been isolated from contaminated mining soil and characterized. Molecular characterization of isolated fungi was performed and amplified sequences were deposited in the GenBank NCBI database. Metal tolerance of the various strains has been determined by measuring the minimum inhibitory concentrations (MICs) and the tolerance indexes of all the tested strains against Cd, Cr, and Pb. Bioaccumulation capacities of Trichoderma harzianum and Komagataella phaffi have also been assessed. These findings helped us find a novel strain of Komagataella phaffi and suggested it to be the potential mycoremediation microbe to alleviate the contamination of Cd, Cr, and Pb. Future studies of this fungal strain can help us to understand its resistance mechanism against other heavy metals, too. Rapidly increasing industry has resulted in greater discharge of hazardous chemicals in the soil. In the current study, soil samples were collected from Nanjing mine (32 degrees 09 ' 19.29 '' N 118 degrees 56 ' 57.04 '' E) and subjected to heavy metal analysis and microbe isolation. A total of 460 fungi were isolated, and five of these were yeast strains. Most of the strains exhibited tolerance to one metal. Five multimetal tolerant strains were selected and identified as Aspergillus sclerotiorum, Aspergillus aculeatus, Komagataella phaffii, Trichoderma harzianum, and Aspergillus niger. Isolated strains were grown in high concentrations of cadmium (Cd), chromium (Cr) and lead (Pb), for induced-tolerance training. The tolerance index (TI) revealed the highest Cd tolerance of novel K. phaffii strain at 5500 ppm (TI: 0.2). K. phaffii also displayed resistance at 4000 ppm against Cr (TI: 0.32) and Pb (TI: 0.32). In contrast, tolerance training for A. niger was not that successful. K. phaffii also displayed the highest bioaccumulation capacity for Cd (25.23 mg/g), Cu (21.63 mg/g), and Pb (20.63 mg/g) at 200 ppm. Scanning electron microscopy (SEM) explored the morphological changes in the mycelia of stressed fungi. Results of this study describe this delicate approach to be species and metal dependent and suggest a potential utilization of this fungal strain for the bioremediation of contaminated soils

Isolation and characterization of pathogen causing brown rot in lemon and its control by using ecofriendly botanicals

Brown rot is a common and devastating disease of different fruits and vegetables. During 2018, a profound brown rot was observed on lemon (Citrus lemon L.) in Islamabad, Pakistan and adjacent areas. This study was designed to identify disease causing pathogen of this disease. Diseased lemon fruit were collected from the orchards and disease causing pathogen was isolated. The morphology of pathogen was examined under stereoscope and compound microscope and the pathogen was identified as Alternaria alternata. For the molecular characterization of this fungus, 18S ribosomal RNA gene was sequenced and its phylogenetic analyses were performed. BLAST analysis revealed 100% similarity with A. alternate NS8, 18S ribosomal RNA gene, partial sequence (MK346034.1). This is the first report of brown rot of lemon, caused by A. alternata in Pakistan. For ecofriendly control of this disease, extracts of indigenous medicinal plants including Justacia adhatoda, Azadriachta indica, Foeniculum vulgare and Mentha spicata were used. In these plant extracts, the presence of various functional groups such as alcohols, carboxylic acids, esters, alkanes and alkenes was revealed by Fourier transform infrared spectroscopy (FTIR). Both in vitro and in vivo assay showed the significant role of aqueous plant extracts to suppress the growth of A. alternata. Among these phytoextracts, A. indica proved to be the most efficient in suppressing the growth of the pathogen and controlling disease. Findings of this study suggest the use of these plant extracts for environment friendly control of fruit rot disease

ZnO Nanoparticle-Mediated Seed Priming Induces Biochemical and Antioxidant Changes in Chickpea to Alleviate Fusarium Wilt

Chickpea (Cicer arietinum L.) is one of the main pulse crops of Pakistan. The yield of chickpea is affected by a variety of biotic and abiotic factors. Due to their environmentally friendly nature, different nanoparticles are being synthesized and applied to economically important crops. In the present study, Trichoderma harzianum has been used as a stabilizing and reducing agent for the mycosynthesis of zinc oxide nanoparticles (ZnO NPs). Before their application to control Fusarium wilt of chickpea, synthesized ZnO NPs were characterized. X-ray diffraction (XRD) analysis revealed the average size (13 nm) of ZnO NPs. Scanning electron microscopy (SEM) indicated their spherical structure, and energy dispersive X-ray analysis (EDX) confirmed the oxide formation of ZnO NPs. Transmission electron microscopy (TEM) described the size and shape of nanoparticles, and Fourier transform infrared (FTIR) spectroscopy displayed the presence of reducing and stabilizing chemical compounds (alcohol, carboxylic acid, amines, and alkyl halide). Successfully characterized ZnO NPs exhibited significant mycelial growth inhibition of Fusarium oxysporum, in vitro. In a greenhouse pot experiment, the priming of chickpea seeds with ZnO NPs significantly increased the antioxidant activity of germinated plants and they displayed 90% less disease incidence than the control. Seed priming with ZnO NPs helped plants to accumulate higher quantities of sugars, phenol, total proteins, and superoxide dismutase (SOD) to create resistance against wilt pathogen. These nanofungicides were produced in powder form and they can easily be transferred and used in the field to control Fusarium wilt of chickpea

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.Y

Resistance associated metabolite profiling of Aspergillus leaf spot in cotton through non-targeted metabolomics.

Aspergillus tubingensis is an important pathogen of economically important crops. Different biotic stresses strongly influence the balance of metabolites in plants. The aim of this study was to understand the function and response of resistance associated metabolites which, in turn are involved in many secondary metabolomics pathways to influence defense mechanism of cotton plant. Analysis of non-targeted metabolomics using ultra high performance liquid chromatography-mass spectrometry (UPLC-MS) revealed abundant accumulation of key metabolites including flavonoids, phenylpropanoids, terpenoids, fatty acids and carbohydrates, in response to leaf spot of cotton. The principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA) and partial least squares discriminant analysis (PLS-DA) score plots illustrated the evidences of variation between two varieties of cotton under mock and pathogen inoculated treatments. Primary metabolism was affected by the up regulation of pyruvate and malate and by the accumulation of carbohydrates like cellobiose and inulobiose. Among 241 resistance related (RR) metabolites, 18 were identified as resistance related constitutive (RRC) and 223 as resistance related induced (RRI) metabolites. Several RRI metabolites, identified in the present study were the precursors for many secondary metabolic pathways. These included phenylpropanoids (stilbenes and furanocoumarin), flavonoids (phlorizin and kaempferol), alkaloids (indolizine and acetylcorynoline) and terpenoids (azelaic acid and oleanolic acid). Our results demonstrated that secondary metabolism, primary metabolism and energy metabolism were more active in resistant cultivar, as compared to sensitive cultivar. Differential protein and fatty acid metabolism was also depicted in both cultivars. Accumulation of these defense related metabolites in resistant cotton cultivar and their suppression in susceptible cotton cultivar revealed the reason of their respective tolerance and susceptibility against A. tubingensis

DataSheet_1_Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis.pdf

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.</p

DataSheet_2_Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis.pdf

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.</p