Disease-Suppressive Soils
Disease-suppressive soils naturally protect crops from pathogens via microbiome-mediated mechanisms. Starting from my PhD research, I worked on establishing a framework for understanding these soils through integrated metagenomics, metabolomics, and microbial ecology approaches. Based on a vast collection of field data and material, I identified taxonomic and metabolic signatures bound to disease suppressiveness (Ossowicki et al. 2020, Proc. R. Soc. B) and deepened these insights by applying functional analysis (Tracanna & Ossowicki et al. 2021, mSystems). The consortium effort was further directed toward designing synthetic communities of bacteria using dilution-to-extinction and genome-resolved synthetic ecology to simplify the suppressive microbiome (Jing, Ossowicki et al. submitted to Science, preprint available). This body of work demonstrated that soil disease suppressiveness is a function of microbial community taxonomic composition, functional composition, inter-strain interactions, and secondary metabolism—providing the mechanistic foundation for engineering beneficial microbiomes.
Microbiome Training : Ecologically Informed Microbiome Engineering
Building on the microbiome perturbation framework (Ossowicki et al. 2021, Environ. Microbiol. Rep.), I developed “microbiome training”—an ecological approach to engineer resilience in native soil communities without introducing nonnative species. This approach leverages niche differentiation, functional redundancy, and microbial diversity to enhance stress tolerance. My Marie Skłodowska-Curie fellowship has advanced this framework toward abiotic stresses. The experimental work highlights the critical importance of secondary metabolites in shaping community structure and function (Pantigoso, Ossowicki et al. 2025, Trends Plant Sci.). A submitted manuscript entitled “Microbiomes in training: enrichment of functions for stress alleviation in plants” presents a framework for this approach (Castañeda et al. submitted to Microbiome, I am last author). This work demonstrates that ecological principles of community assembly and succession can be harnessed to condition soil microbiomes for enhanced plant performance under environmental constraints—a paradigm shift toward context-specific, sustainable agricultural solutions.
Effects of Biobased Plastics on Soil Microbiomes
As agricultural practices adopt novel materials (e.g., biodegradable plastic mulches), understanding how these substances alter soil microbiome function is critical. I have contributed to investigations of how plastic mulch film residues affect soil properties and microbiomes (Qi, Ossowicki et al. 2020 and 2022). Currently, I am preparing a manuscript examining the effects of novel plant–based bioplastics on soil microbiome composition and function. This research area is particularly relevant as the agricultural sector transitions toward sustainable alternatives to conventional inputs—and essential for predicting unintended ecological consequences. These projects create valuable opportunities for both academic and industry collaboration.