Daniel Legesse

Metataxonomic investigations of Champagne grapevine microbiome (soil, rhizosphere, phyllosphere, Carposphere):

· Sampling from different plant compartments and vineyard environments.

· DNA extraction and quality control.

· Amplicon sequencing (16S rRNA for bacteria, ITS for fungi) using Illumina platforms.

· Bioinformatics processing (quality filtering, OTU/ASV clustering, taxonomy assignment, diversity and differential abundance analysis).

· Network and co-occurrence analysis to reveal keystone taxa.

Shotgun metagenomics studies to complement amplicon data:

· DNA library preparation and whole-metagenome sequencing.

· Assembly, annotation, and functional gene prediction.

· Taxonomic and functional analysis to identify species and functional traits associated with grapevine health and disease suppression.

Microbiome-driven BCA development:

· Identification of microbial taxa with central ecological roles and potential antagonistic functions against Plasmopara viticola.

· Guided isolation of candidate microbes, focusing on Bacillus spp. and other promising taxa.

· Characterization and identification of isolates through morphology, biochemical tests, and molecular sequencing.

In vitro and greenhouse screening of BCAs:

· Antagonistic assays against P. viticolazoospores.

· Testing both single strains and microbial consortia.

· Evaluating plant protection effects in planta under controlled greenhouse conditions.

Mode of action studies:

· Direct inhibition of P. viticolazoospores.

· Indirect inhibition through induced systemic resistance (ISR) in grapevine.

Molecular plant–pathogen interaction studies:

· qPCR assays for monitoring grapevine defense gene expression after BCA application.

· Digital droplet PCR (ddPCR) for precise quantification of Plasmopara viticola biomass in infected plant tissues.

Integration of multi-omics and experimental data:

· Correlating metataxonomic and metagenomic findings with experimental BCA performance.

· Linking microbial community structure and function to pathogen suppression mechanisms.

· Establishing a framework for targeted BCA development in sustainable viticulture.

Focus on Plant–Microbe Interaction Research Activities including the following subjects:

· Microbiome investigations in the sorghum rhizosphere to study the tripartite interaction between Striga hermonthica, mycorrhizal fungi, and sorghum.

· In vitro assays to evaluate microbial effects on Striga seed germination, haustorium formation, and attachment to sorghum roots.

· Volatile-mediated suppression studies: analysis of microbial and plant volatile organic compounds (VOCs) in regulating Striga seed germination and early parasitic development.

· Root exudate modification assays: testing chemical and microbial treatments that alter sorghum root exudate composition to suppress Striga germination and haustorium initiation.

· Greenhouse infection assays for Striga–sorghum interactions:

· Establishment and management of infection assays (watering, thinning, nutrient management using Hoagland solution).

· Quantifying Striga emergence and attachment on sorghum roots.

· Biocontrol candidate (BCA) screening and evaluation:

· Collection and preparation of fungal spores and beneficial microbial inocula.

· Pathogenicity tests of microbial isolates against Striga attachment on sorghum.

· Screening of microbial isolates and consortia for growth-promoting and Striga-suppressing potential in controlled conditions.

· Soil and microbial enzyme studies related to Striga–sorghum interactions: quantitative and qualitative assessment of microbial enzyme activity, protein estimation, and metabolite profiling.

· Innovative fertiliser solutions and microbial formulations aimed at reducing Striga infestation in sorghum fields.

· Pathogen–parasite–host interaction studies:

· Exploring the effect of Fusarium spp. and other antagonists on Striga germination and attachment.

· Identification of microbial phenotypes in vitro with activity against Striga and their role in shaping the sorghum rhizosphere

Focus on Plant–Microbe Interaction Research Activities including the following subjects:

· Sorghum microbiome and plant growth studies:

· Investigating sorghum rhizosphere microbiome structure and its role in nutrient uptake and stress tolerance.

· Functional analysis of plant growth–promoting endophytes and rhizobacteria to enhance sorghum growth and resilience.

· Effects of phytobeneficial soil microbes on nutrient acquisition and stress tolerance in sorghum and finger millet under low-input sustainable agriculture systems.

· Bt cry gene characterization:

· Molecular characterization of Bt cry genes.

· Evaluating their impact on bollworm growth and development in cotton.

· Microbial enzymes, metabolites, and proteins:

· Investigating microbial enzyme activity, protein estimation, and metabolite profiling.

· Characterizing microbial enzymes, secondary metabolites, and proteins involved in biosynthetic pathways and signaling.

· Studying microbial–entomopathogen symbiosis interactions.

· Soil organic matter and carbon dynamics:

· Characterization of soil organic matter composition and functional role in ecosystem services.

· Identifying signatures of soil core microbiome and its interaction with host plants.

· Phytobeneficial microorganisms and soil engineering:

· Application of plant-beneficial microbes for sustainable agriculture and soil engineering.

· Screening of microbial isolates for plant growth–promoting and weed-suppressive traits.

· Novel microbial resources from diverse environments:

· Exploring extremophilic environments (forests, wetlands, volcanic areas, hot springs, and water bodies) in Ethiopia for the discovery of novel microbial products.

· Identifying microbial isolates with antimicrobial activity against plant pathogens.

· Molecular characterization of novel rhizobia from Ethiopian legumes for biofertilizer development.

· Molecular plant–pathogen studies:

· Genetic diversity analysis of Xanthomonas campestris pv. musacearum (XCM) isolates from enset production areas.

· Development of microbial secondary metabolite–based BCAs against African fall armyworm (FAW).