Isolation of Soil Microorganisms Using iChip Technology
January 10th, 2025
The iChip technique makes use of an inexpensive and simple in-situ isolation device that increases the rates of novel microorganism discovery from the soil. Novel microorganisms can be used for further study pertaining to the soil microbiome or natural product discovery, amongst other applications.
We are attempting to discover new types of chemistry to combat agricultural pathogens. Using iChip technology, we have isolated novel organisms, which we hope will lead to new chemistry. Testing these organisms and/or their natural products against agricultural pathogens potentially lead to finding new biopesticide candidate organisms and/or compounds.
The iChip method allows us to isolate microorganisms that are unculturable under conventional conditions by providing a period of domestication and contact with their natural environment. Our modified iChip build is simple, inexpensive, and reduces the risk of microbial contamination, making it easily accessible for a variety of research goals. Our iChip results open questions like what mechanisms drive pathogen suppression by novel microbes?
Can these bioactive compounds perform reliably in real-world trials? How do environmental factors influence their efficacy? Addressing these questions will guide sustainable biopesticide development, transforming plant disease management, and reducing reliance on synthetic fungicides.
The lab will apply iChip technology to isolate novel bacteria from disease suppressive soils produced through cover cropping, identifying novel microbes and bioactive compounds. These will be tested in controlled plant disease studies to develop innovative, sustainable alternatives to synthetic fungicides for managing agricultural diseases. To construct a modified iChip using a 5 millimeter agar punch tool, remove the bottoms of the wells from a 96-well plate.
Cut 0.05 micrometer polycarbonate membranes into rectangles, ensuring the dimensions match the bottom area of a 96-well plate. Apply a silicone sealant to adhere the polycarbonate membrane to the bottom of the 96-well plate. Ensure the adhesive seals the wells but does not entirely cover the openings of the wells.
Allow the plates to dry for 24 hours. Add 4.5 milliliters of sterile water to each of the 15 milliliter centrifuge tubes labeled A to D, and to each of the 50 milliliter tubes labeled E to H.Add 1 gram of soil into a 50 milliliter centrifuge tube. Then add 10 milliliters of water to the tube and vortex the mixture for 10 minutes.
Allow the soil suspension to settle for 10 minutes. Next, pipette 0.5 milliliters of the soil supernatant into tube A and mix thoroughly. Now, transfer 0.5 milliliters of the cell suspension from tube A to tube B and mix thoroughly.
Repeat for all remaining centrifuge tubes, completing a series of tenfold dilutions across the eight tubes. To begin, submerge the iChips completely in 95%ethanol. After 15 minutes, remove the plates from the ethanol and place them on a sterile paper towel in the laminar flow hood.
Allow the ethanol to evaporate while turning on the ultraviolet sterilizer in the laminar flow hood for 15 minutes. Pipette 360 microliters of sterile succinate minimal salts or SMS media into the first column of the plate to serve as a control. Add 45 milliliters of SMS to the cell suspension in tube E.Mix thoroughly to combine the cell suspension with the agar.
Pipette 360 microliters of the agar cell mixture into all remaining wells of the 96-well plate. Once the media is set, seal the top of the plate with a PCR plate cover. Fill the plates using tubes F, G and H to prepare a total of four plates with tenfold differences in concentrations.
Place the plates in a container containing approximately 1 inch of soil with the membrane side facing down. Incubate the plates inside the covered container in the dark at 25 degrees Celsius. After six weeks, examine the iChips for microbial growth.
Rinse the modified iChip three times with sterile water to remove all soil particulates. Wipe the top and sides of the plate with 95%ethanol, avoiding the side with the semipermeable membrane. Using a sterile blade, cut through the plate cover around a well containing a colony, and remove the square with sterile tweezers.
Using a sterile streaking tool, pierce the colony and streak onto the SMS agar plate with the four quadrant method. Incubate the plates at 25 degrees Celsius for one week or until colony growth is observed. After incubation, examine the colonies to confirm the isolation of cultures.
Overview
The iChip technique facilitates the discovery of novel microorganisms from soil, enhancing research in soil microbiomes and natural product discovery. This method allows for the isolation of unculturable microorganisms, potentially leading to new biopesticide candidates.
Key Study Components
Area of Science
- Microbiology
- Soil Science
- Biotechnology
Background
- Novel microorganisms can contribute to sustainable agriculture.
- The iChip method provides a way to culture previously unculturable microbes.
- Understanding microbial interactions can lead to innovative pest management strategies.
- Research aims to reduce reliance on synthetic fungicides.
Purpose of Study
- To isolate novel bacteria from disease-suppressive soils.
- To test these microorganisms against agricultural pathogens.
- To develop sustainable alternatives to synthetic fungicides.
Methods Used
- Modified iChip construction for microbial isolation.
- Soil sample preparation and dilution series.
- Incubation of iChips in natural soil environments.
- Colony isolation and characterization on agar plates.
Main Results
- Successful isolation of novel microorganisms using the iChip method.
- Identification of potential biopesticide candidates.
- Insights into the mechanisms of pathogen suppression by isolated microbes.
- Establishment of a protocol for future microbial studies.
Conclusions
- The iChip technique is effective for discovering novel soil microorganisms.
- Research findings may transform plant disease management practices.
- Further studies are needed to evaluate the efficacy of identified compounds in real-world applications.
Frequently Asked Questions
Executive Industry Relevance
The iChip technology enables the isolation of previously unculturable soil microorganisms, expanding the accessible diversity for natural product discovery and biopesticide development. This approach addresses a critical bottleneck in early discovery by unlocking new sources of bioactive molecules relevant to combating antimicrobial resistance and agricultural pathogens. Integrating iChip-derived isolates into R&D pipelines enhances predictive confidence in identifying novel chemistries and supports risk-adjusted portfolio advancement.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables access to novel microbial diversity for therapeutic hypothesis generation.
- Supports biological de-risking by expanding the pool of candidate organisms and chemistries.
- Facilitates functional validation of microbial-derived bioactive compounds against target pathogens.
- Improves predictive confidence in early-stage screening for new biopesticide leads.
Screening & Assay Development
- Provides a reproducible workflow for preparing validated microbial isolates for downstream assays.
- Supports standardization and scalability in screening for antimicrobial or biopesticide activity.
- Enables quantitative assessment of microbial growth and bioactivity in controlled conditions.
- Prepares isolates for reliable compound evaluation and secondary characterization.
Translational & Preclinical Research
- Aligns with translational goals by generating candidate microbes and compounds for real-world efficacy testing.
- Supports continuity from discovery through preclinical validation in plant disease models.
- Enables risk-adjusted advancement of promising biopesticide candidates based on mechanistic insights.
- Facilitates the study of environmental and ecological factors influencing compound performance.
Pipeline & Workflow Integration
The iChip method fits at the interface of early discovery and lead identification, providing a bridge from environmental sampling to preclinical candidate selection.
- Discovery Biology: Expands hypothesis testing by enabling isolation of novel microbes and their metabolites.
- Screening: Delivers standardized, reproducible microbial isolates for high-confidence screening workflows.
- Analytics: Supports quantitative measurement of microbial growth and bioactivity for comparative analysis.
- Translational Research: Connects discovery-stage isolates to preclinical efficacy studies in disease-relevant systems.
- Enterprise Reuse: Establishes a reusable platform for ongoing natural product and biopesticide discovery efforts.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence and reduces mechanistic ambiguity in early-stage discovery.
- Operational Value: Offers a standardized, scalable, and low-contamination workflow for microbial isolation.
- Strategic Value: Enables better go/no-go decisions and capital efficiency by expanding the accessible chemical space.
- Portfolio Impact: Supports risk-adjusted prioritization of novel microbial candidates for further development.
Implementation Considerations
- Requires expertise in microbiology, soil science, and sterile technique.
- Needs access to basic laboratory infrastructure and analytical tools for microbial characterization.
- Demands cross-team standardization for reproducibility and data comparability.
- May require adaptation for different soil types or environmental conditions.
- Dependent on effective downstream screening and validation to realize full R&D value.
