Projects | Freilich Lab

Bioremediation

Development of a simulation platform for enhancing biodegradation of hydrocarbons in soil and wasteland
BTEX contaminants
Pesticides in soil

Microbiome functioning in agroecosystems

Design of organic soil amendment treatments for ARD
Suppression of post-harvest pathogens.
Optimization of Phosphorous utilization
Trophic interactions with mesofauna

Emissions

Upgrading waste-derived biogas production
Management of GHG in wetlands

Modeling based design of soil amendments that lead to enhanced biodegradation of soil pollutants including hydrocarbons, BTEX and herbicides

In a recent series of works, we provided pioneering evidence, validated in-vitro and in-situ, that CBM-based predictions can guide the development of strategies for microbiome management where our case study concerned the optimization of selected function-enhanced biodegradation of agricultural pollutants and BTEX contaminants.

Selected bioremediation publications:

Our approach for modeling and harnessing native communities (from Faust et al):

Nowadays, we are testing the application of the approach towards several practical solutions including ex situ and in situ bioremediation of hydrocarbons.

We are part of the Green Soil consortia of the Israeli Authority of Innovation. Jenny Yusim & Shlomit Medina are working on this project, supported by Gon Carmi from the Bioinformatics unit.

Management of the soil microbiome in cropping agro-ecosystems

The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. We apply genomic-based algorithms to formulate testable hypotheses for strategically engineer the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities.

A framework for genomic-based delineation of functionalities and exchanges in the microbiome (Figure is taken from Ginatt et al., 2024)

Key projects where we apply the framework include:

Design of organic soil amendment treatments for Apple Replant Disease

We apply this framework to reduce unpredictable elements in amendment-based solutions that replace chemical-based treatment. Better understanding of a beneficial root microbial function is critical for the development of ecologically-sound methods through the directed targeting of specific groups.

In the works and video below, we demonstrated how we used genomic-based algorithms to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities.

Shaya Bem and Michael Rachmilevich are working on this project. They are introducing a hybrid sequencing approach to improve metagenome assembly and implementing metabolomics into the metabolic network models.

The project is a collaboration with Prof. Mark Mazzola, Tracey Somera and Elisa Korenblum. The project is supported by BARD.

Phosphorous Solubilizing microorganisms (PSM) and their role in improving plant biomass

Phosphorus is an essential but often limiting nutrient in soils, with much of it locked in forms unavailable to plants, creating a major constraint for agricultural productivity. This project addresses that challenge by examining how rhizosphere microbial communities may influence plant phosphorus acquisition and growth across contrasting soil environments. By using an experimental system (Ran Erel Group & Hanan Eizenberg group) designed to study the role of soil microbiota in supporting phosphorus solubilization, we aim to uncover trends, interactions and conditions assisting this function, essentially contributing to more sustainable agricultural and crop production strategies.

Alon Avraham Ginatt & Asaf Salmon are working on this project, supported by Gon Carmi from the Bioinformatics unit. The project is supported by ICL.

Biological control of post-harvest pathogens

Genomic technologies have provided new insights on the process of disease progression leading to the emergence of a holistic view. The newly emerging 'pathobiome' concept suggests a conceptual shift from the one pathogen - one disease concept of Koch’s postulates, established in the pre-(meta)genomic era. The term “pathobiome” was coined to describe a consortium of microbial species that interact with each other and the host to foster pathogenicity and the development of a disease. The concept of the “pathobiome” originally emerged from research on the human microbiome and suggested that dysbiosis of a balanced and diverse microbial community structure is always aligned or correlated with an unhealthy condition. Similarly, a healthy plant is typically associated with a diverse and stable community structure, described as a symbiome, that plays an essential role in its growth and function. A shift from a symbiome to a pathobiome occurs during the onset of disease, and usually involves major compositional transitions leading to pathogen proliferation and disease development. As such, the pathobiome concept provides a more holistic and realistic view of disease development, where complex assemblages of organisms are involved. In the context of postharvest disease, no efforts have been made thus far to identify and functionally investigate the pathobiome of postharvest diseases. We predict that understanding the symbiome and formation of the pathobiome will become a crucial element for mitigating disease in global food production systems. In a collaboration with Samir Droby, we apply genomic-based modeling approaches to explore the role of the microbial community in disease progression aiming at the development of guided strategies for chemical-free disease suppression.

Rotem Bartuv is working on this project supported by Gon Carmi from the Bioinformatics unit.

Read about our vision in our publications below:

The pathobiome concept applied to postharvest pathology and its implication on biocontrol strategies

Biological Control of Postharvest Diseases: The Evolution of New Concepts and Perspectives

The project is supported by ISF.

Management of greenhouse gas emissions in natural and artificial systems

Methanogenesis is a biological process where methane is produced by microorganisms. The process starts with anaerobic microorganisms that break down organic matter by hydrolysis and fermentation and together with syntrophic bacteria turn it into acetic acid, CO2 and H2, which are utilized by methanogenic archaea (methanogens) to produce methane. Understanding the processes involved in methane production can serve as a key for properly managing methane production - reducing emissions of greenhouse gas, on the one hand, and optimizing its use as an energy source on the other hand. Despite the abundant information on the existence of the metabolism of the methanogenic process, the syntrophic relationships between the microorganisms are still not clearly understood. We apply our computational approaches to explore two relevant processes where methanogenesis is critical:

Upgrading biogas production in wastewater treatments
Study greenhouse gas emission management from wetlands

The project is a collaboration with Keren Yanuka-Golub (Galilee Society Institute of Applied Research). Jenny Yusim, Raphy Zarecki & Julia Ghantao worked on this project, supported by Shlomit Medina and Gon Carmi from the Bioinformatics unit.