In Situ Cultivation Devices: Unlocking the Hidden Majority of Microbial Life

In situ cultivation devices are tools designed to isolate and grow microbes directly within their natural environments, rather than transporting them to an artificial, nutrient-rich laboratory setting.

These devices allow microbes to experience the same physical, chemical, and biological conditions they would encounter in soil, sediments, water, or host tissues. By doing so, they overcome many limitations of traditional culturing methods.

1. Diffusion Chambers

• Early versions of in situ cultivation.
• Typically consist of a small chamber enclosed by semi-permeable membranes.
• The chamber contains a diluted microbial inoculum in agar or liquid media.
• When placed in the environment (e.g., buried in soil), nutrients and signaling molecules diffuse in, while cells remain trapped.
• This setup allows microbes to interact chemically with their environment while still being physically isolated for later recovery.

2. iChip (Isolation Chip)

• A breakthrough device developed by the lab of Slava Epstein and commercialized by companies like NovoBiotic.
• The iChip contains hundreds of tiny wells inoculated with single bacterial cells from environmental samples.
• The entire chip is sandwiched between diffusion membranes and reinserted into the environment (e.g., buried in soil).
• After incubation, colonies that grow in situ can be transferred to lab conditions for further study.
• The iChip was crucial in the discovery of teixobactin, a new antibiotic from an uncultured soil bacterium (Eleftheria terrae).

3. Micro-Porous Substrate Devices

• Utilize porous materials like hydrogels or ceramic supports to mimic micro-scale environments.
• Designed to retain cells while allowing nutrient flow and chemical signaling.
• Often used for marine and sediment microbiome studies.

Native conditions preserved: pH, redox potential, oxygen levels, and nutrient gradients are maintained.

Natural chemical cues: Many microbes require signals or metabolites produced by neighboring species to grow signals missing in lab media.

Reduced stress: Microbes are not forced to adapt to artificial conditions, improving survival and culturability.

Allows for slow growers: Many rare or slow-growing microbes are outcompeted in rich lab media. In situ devices prevent this by providing lower nutrient levels more reflective of natural settings.

Natural product discovery: Access to uncultured microbes increases the chance of finding novel antibiotics, enzymes, and secondary metabolites.

Microbiome studies: In situ methods help isolate elusive members of human, animal, or plant microbiomes.

Biotechnology and synthetic biology: New strains can be incorporated into bioengineering pipelines for drug production, waste degradation, and more.

Environmental microbiology: Enables cultivation of microbes from extreme or complex environments (e.g., deep sea, Arctic soils).

Scalability: While promising, devices like the iChip are still limited in throughput compared to automated lab systems.

Recovery: Not all microbes that grow in situ can be maintained in lab conditions afterward.

Standardization: Variability in device design, materials, and deployment makes reproducibility a challenge.

Integration with omics: Future tools could combine in situ growth with real-time monitoring of gene expression and metabolite production.