Biology subjects

Ghadamgahi, F.

Publications and source records attributed to Ghadamgahi, F..

8 recordsLinked to original sources

bioRxiv2024

Evaluating the Biocontrol Potential of Pythium oligandrum and Serratia proteamaculans in Controlling Phytophthora plurivora in European beech (Fagus sylvatica)

In recent years, the plant pathogen Phytophthora plurivora has caused severe damage to beech forests in many European countries, including Sweden. In many affected areas, few protective measures are in place due to fears about potential negative impacts on the ecosystem or public health. The research presented in this article assesses the biocontrol potential of the oomycete Pythium oligandrum and the bacterium Serratia proteamaculans against P. plurivora, with experiments performed under both in vitro and greenhouse conditions, which could represent a step forward in developing a safe treatment for European beech forests. The in vitro results revealed that P. oligandrum and S. proteamaculans significantly inhibited pathogen growth and stimulated a shift in the hyphal growth pattern towards shorter, branched hyphae with many hyphal swellings and thickened cell walls. The experiments conducted in greenhouses showed that treating three-month-old beech seedlings with P. oligandrum and S. proteamaculans counteracts the P. plurivora pathogen and reduces disease symptoms on the aerial and underground parts of the plant. GC-MS analysis detected the volatile organic compounds alpha-pinene, 2,5-dimethyl-pyrazine, and 3-methyl-1-butanol from S. proteamaculans; these compounds have the potential to inhibit pathogen growth. The disease suppression demonstrated by these biocontrol agents could thus be related to the synergistic effect of competition for nutrients with the secretion of hydrolytic enzymes and VOCs; moreover, induced systemic resistance may be triggered under greenhouse conditions. In conclusion, using P. oligandrum and S. proteamaculans could represent an environmentally friendly strategy for effectively controlling the disease caused by P. plurivora in beech.

pathology↗

bioRxiv2024

Genetic Diversity of Zymoseptoria tritici Populations in Central and South-eastern Ethiopia

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is a serious threat to global wheat production, and a major bottleneck to wheat production in Ethiopia. Accurate identification and analysis of the pathogens genetic structure helps inform robust STB management. This study analyzed the molecular identity and genetic structure of 200 Z. tritici isolates retrieved from diseased crops in central and south-eastern regions of Ethiopia. Allelic diversity at 12 simple sequence repeat (SSR) loci was examined for all 200 isolates, and 165 isolates were identified by Sanger sequencing of the internal transcribed spacer (ITS) region of nuclear DNA (rDNA) region. The microsatellites were highly polymorphic, with mean number of alleles (Na) = 6.23, effective alleles (Ne) =2.90, Neis gene diversity (H) =0.57, and polymorphic information content (PIC) =0.59, and an analysis of molecular variance confirmed the presence of low population differentiation (Fixation Index (FST) = 0.02, Gene Flow (Nm) = 14.7), with 95% of the total genetic variation residing within populations, and only 5% residing between populations. The highest genetic diversity (Number of allele (Na) = 9.33, Effective number of allele (Ne) = 3.41 and Neis gene diversity (H) = 0.68) was observed in the Oromia special zone surrounding Finfinnee (OSZ) Z. tritici populations, followed by Arsi and North Shewa populations, indicating that these areas are ideal for multi-location germplasm resistance screening, and also pathogen genetic and genomic analyses. Cluster analyses did not clearly divide the populations into genetically separate clusters according to their geographic sampling areas, probably because of high gene flow. All individual samples showed genetic admixture, and shared genomic backgrounds from two subgroups (K=2). Overall, the SSR markers proved to be highly informative and effective genetic tools for unlocking the pathogens genetic structure. The Z. tritici populations of central and southeast Ethiopia exhibit high genetic diversity, indicating the need to deploy durable and diverse disease management strategies. North Shewa, OSZ, Arsi and West Arsi administrative zones represent hotspots for genetic and genomic analyses of Z. tritici. Moreover, these areas would be excellent locations for host-pathogen interaction studies, and wheat germplasm screening for STB resistance.

plant biology↗

bioRxiv2024

Genomic loci for sclerotinia stem rot resistance and chlorophyll stability in Brassica napus: integrating GWAS with microbiome insights

Sclerotinia Stem Rot (SSR) disease is one of the most serious diseases affecting the yield and quality of oilseed rape (Brassica napus). Understanding the genetic basis of the resistance trait in oilseed rape to SSR and microbiome composition for enhanced resistance is crucial for developing resistant varieties and sustainably mitigate the impact of the disease. In this study, in a panel of 168 oilseed rape accessions, most resistant (NGB 13503 and NGB 13834) and susceptible (NGB 13497 and NGB 13897) accessions are identified. A Genome-wide association study (GWAS) identified 47 SNPs linked to the SSR lesion length, lesion area, and lesion relative to the leaf area. Among the SNPs significantly linked to lesion length were Bn-A04-p10555408, Bn-A07-p12487549, Bn-A09-p4652268, Bn-A09-p4916858 and to our knowledge, these SNPs have not been previously linked to SSR resistance in oilseed rape. Moreover, the study identified 24 SNPs linked with chlorophyll content before SSR inoculation (SPADH), after the SSR inoculation (SPADI), and chlorophyll index (CI). Maintaining the chlorophyll level is correlated with the SSR resistance. Furthermore, bacterial taxa (e.g. Pseudomonas, Methylobacterium, and Aquabacterium) and fungal taxa (e.g. Mycosphaerellales, Thelebolales, and Akanthomyces) were enriched in the resistant compared to in the susceptible oilseed rape accessions. The SNPs linked to lesion length showed consistent haplotype variation between these selected accessions. Given the absence of complete resistance against SSR, the study provides insights into the significance of maintaining chlorophyll levels and considering microbiome composition for enhancing the level of existing partial resistance to SSR in oilseed rape.

plant biology↗

bioRxiv2024

Genomic Insights and Biocontrol Potential of Ten Bacterial Strains from the Tomato Core Microbiome

Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. These taxa included some that are commonly used as biofertilizers and biocontrol agents (Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. This yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. The gathered genomic information will be instrumental in planning the use of these bacteria individually or in consortia to enhance plant growth by coupling strains with different traits, effects, and mechanisms of action.

genomics↗

bioRxiv2024

Plant Development Drives Dynamic Shifts in the Root Compartment Microbiomes of Wild and Domesticated Finger Millet Cultivars

BackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plants developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages. ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples were Proteobacteria, Actinobacteria, and Bacteroidetes, while the dominant fungal phyla were Ascomycota and Basidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance of Actinobacteria in the endosphere was accompanied by a reduced abundance of Proteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genus Pseudomonas. Moreover, the host plants developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plants developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.

microbiology↗

bioRxiv2024

Extracellular biosynthesis of silver nanoparticles using cell suspension of Rhodococcus fascians

Biosynthesis of metallic nanoparticles using biological systems such as bacteria has become an important nanobiotechnology area. In this report, we present the first extracellular biosynthesis of silver nanoparticles (AgNPs) using the gram-positive bacterium Rhodococcus fascians. The AgNPs underwent characterization through various analytical techniques, encompassing UV-visible spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Transmission electron microscopy (TEM) and Scanning electron microscopy (SEM). UV-visible spectroscopy revealed the emergence of an absorbance peak at 430 nm due to the synthesis of AgNPs. R. fascians started producing AgNPs after 12 h of incubation, with the highest yield after 48 h. The extent of synthesis was higher when cultures were grown in the dark than in the light. According to TEM and SEM, the AgNPs had a uniform spherical morphology of diameter 10-80 nm. The AgNPs exhibited antifungal efficacy against the virulent filamentous fungi Rhizoctonia solani, Botrytis cinerea, and Fusarium graminearum, which cause root rot, soft rot and head blight on plants, respectively. This research provides evidence on the ability of R. fascians to generate AgNPs from silver nitrate, as well as their subsequent assembly and potential for controlling vascular wilt disease.

microbiology↗

bioRxiv2023

Comparative Transcriptome Profiling Provides Insights into the Growth Promotion Activity of Pseudomonas fluorescens strain SLU99 in Tomato and Potato Plants

The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.

plant biology↗

bioRxiv2021

Spray-induced gene silencing as a potential tool to control potato late blight disease

Phytophthora infestans causes late blight disease on potato and tomato and is currently controlled by resistant cultivars or intensive fungicide spraying. Here, we investigated an alternative means for late blight control by spraying potato leaves with double-stranded RNAs (dsRNA) that target P. infestans genes that are essential for infection. Through confocal microscopy, we show that the sporangia of P. infestans expressing Green Fluorescent Protein (GFP) can take up in vitro synthesized dsRNAs homologous to GFP directly from their surroundings, including leaves, which leads to the reduced relative expression of GFP. We further demonstrate the potential of spray induced gene silencing (SIGS) in controlling potato late blight disease by targeting developmentally important genes in P.infestans such as guanine-nucleotide binding (G) protein {beta}-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-{beta}-glucanase (PiEndo3). Our results demonstrate that SIGS can be potentially used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes.

plant biology↗