Environmental microbiomes, ecosystem resilience and predictive microbial ecology

Environmental microbiomes across natural and managed ecosystems

We investigate microbial communities associated with soils, plants, water, marine organisms, algae, insects and other environmental reservoirs, asking how environmental conditions, host biology and ecological interactions shape community assembly and function. By integrating microbiome profiling with environmental chemistry, ecological characteristics and host phenotypes, we seek to identify reproducible microbial signatures associated with environmental stress, ecosystem disturbance and biological resilience.

A major component of this effort is the Plant and Soil Microbiome Project, a large-scale research and education initiative that links plant identity, soil properties, geography and microbial community composition. Within this citizen-science framework, high-school students participate in authentic scientific research, from sampling and experimental design to data analysis, while contributing to the generation of large, standardised microbiome datasets. This distributed sampling strategy enables broad ecological comparisons across habitats while expanding participation in environmental microbiome research.

In parallel, we investigate microbiome responses to environmental stress in agricultural and natural ecosystems. Within the Horizon Europe WHEATWATCHER project, we analyse wheat-associated microbiomes across European field sites and in controlled greenhouse experiments in which plants are exposed to salinity, nutrient imbalance, petroleum-derived contaminants, heavy metals and microplastics. We also participate in national biodiversity initiatives by characterising microbial communities across diverse Israeli habitats and environmental collections, including work associated with the Israeli Biodiversity Curation Centre (IBCC) and the Israel National Culture Collection of Algae (INCCA). Together, these studies seek to understand how environmental change reshapes microbial communities and to establish microbiome-based indicators for long-term ecosystem monitoring.

High-resolution microbiome technologies for environmental research

Many ecological questions are currently limited by the taxonomic resolution and scalability of conventional microbiome methods. To overcome these limitations, we develop new molecular and computational approaches for high-resolution microbiome profiling across diverse environmental sample types. These include the CoSMIC framework for microbial community reconstruction and computational methods for integrating large-scale sequencing datasets. Our goal is to provide accurate, scalable tools that enable comparative microbiome research across ecosystems and facilitate the development of microbiome-based diagnostics for agriculture, biodiversity monitoring and environmental management.