Farideh Ghadamgahi

Fungal wilt disease caused by Fusarium oxysporum is one of the bottlenecks to the productivity of chili pepper (Capsicum annuum L.) in Ethiopia and around the globe. There is little extensive molecular research on the identification of the pathogen in Ethiopia, and it is difficult to predict the severity of the disease. Thus, the objective of this study was to identify virulent Fusarium species and estimate their disease severity in one of the main Capsicum annuum producing areas of Ethiopia. The incidence of chili pepper wilt disease was monitored for three consecutive years (2020–2022) from mid-October to December. In this study, we applied a combined approach (Disease symptoms, as well as culture-based, microscopic, and molecular barcode assessments) for the identification of F. oxysporum. Multiple linear regression analysis revealed that the plant disease incidence monitored over the three years predicted plant disease severity with an accuracy of 59.79% (R2 = 0.5979, p < 0.10). Similarly, Pearson correlation analysis linking Fusarium wilt incidence and severity revealed a statistically significant positive correlation (r = 0.694). However, a correlation heat-map indicated that the highest plant disease incidence recorded in the 2022 season was not necessarily associated with the highest disease severity. Nucleotide sequence analysis of the fungal internal transcribed spacer (ITS) region allowed us to identify 12 virulent pathogens (F. oxysporum). As long as the nature of the disease, host immunity, inconsistency between surveyors, temperature, and moisture are taken into consideration, continuous surveillance of plant disease incidence can be utilized to predict disease severity.

Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses.

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 pathogen’s 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, Nei’s 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 (F _ST ) = 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 Nei’s 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 pathogen’s 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.

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.

Background: Plant-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 plant’s 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. Results: Our 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 plant’s developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. Conclusions: Our 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 plant’s 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.

P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.

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 the P. infestans genes essential for infection. First, we showed 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 led 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 protein β-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-β-glucanase (PiEndo3). Our results demonstrate that SIGS can potentially be used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes. [ ] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .