A tiny lens into the vast world of soil microbes
Microorganisms behave differently in the lab, so researchers designed nanocultures to cultivate them in their natural environment. Magnetic shells provide an efficient way to retrieve them.
An estimated one trillion species of microorganisms reside on Earth, yet scientists have been able to study less than two percent of them. Because many microorganisms cannot be cultivated in laboratories, researchers at Carnegie Mellon University are creating technology to cultivate them in the field.
Better tools for culturing previously unknown microbial species may lead to novel antibiotics or other therapeutic products. Tagbo Niepa developed a microcapsule system to cultivate microorganisms in their natural environment, rather than in laboratory conditions, where they behave differently.
Because each microcapsule can hold a nanoliter volume of microbial culture, these tiny bioreactors are referred to as “nanocultures.” Microorganisms natively found in soil, for example, can be sequestered inside nanocultures, which can then be put back into the soil.
Once the nanocultures are placed in soil or another environment, researchers need an efficient and targeted way to retrieve them. Niepa, associate professor of chemical engineering and biomedical engineering, and collaborators designed nanocultures that can be moved with a magnet. In Science Advances, they show proof of concept for using magnetically-responsive nanocultures to cultivate microorganisms.
Huda Usman, a Ph.D. student in chemical engineering, functionalized the polymer shells with magnetic iron oxide nanoparticles. Adding nanoparticles to a polymer matrix usually decreases its transparency. In thicker membranes, this is a problem for researchers trying to observe microbial growth. Because nanoculture shells are so thin, however, light can diffuse through even when the shells contain magnetic nanoparticles. This means that researchers can still see inside magnetic nanocultures using standard light microscopes and fluorescence microscopes.
Source: Tagbo Niepa
A: A schematic illustration showing how magnetically-responsive nanocultures are created using a microfluidic device. In this system, three liquid phases—a bacterial suspension (W), a polymer mixture containing magnetic nanoparticles (O), and an outer stabilizing solution (W)—are brought together to form water-in-oil-in-water (W/O/W) emulsions. These are then solidified into robust capsules, each encapsulating bacteria within a semi-permeable magnetic shell. B, C: Scanning Electron Microscopy (SEM) images of the resulting nanocultures show their uniform size, spherical shape, and intact shell structure, demonstrating successful and consistent fabrication at the microscale.
Niepa and Usman’s study demonstrates that nanoculture shells remain selectively permeable when magnetic nanoparticles are added. This is essential to the technology, which is designed so that microorganisms can continue the nutrient exchange, waste removal, and cross-communication processes they rely on.
The findings also show that magnetic nanocultures are not toxic for microbial cells. “The system holds the nanoparticles in the shell so that the cells are not directly exposed,” says Niepa. “Even if they were directly exposed to the magnetic nanoparticles, the concentration that we use does not inhibit cell growth.”
Source: Tagbo Niepa
Green Fluorescent Protein (GFP)-tagged Pseudomonas aeruginosa was encapsulated inside red-stained, magnetically functionalized nanocultures. Growth was monitored using confocal microscopy to explore how the microbes respond to different environmental conditions—acidic (pH 2, left) and neutral (pH 7, right)—mimicking scenarios like acid rain and freshwater lakes.
After optimizing the microcapsule design for cell cultivation, Usman tested the magnetic response. She first used a magnet to move hollow nanocultures. Then, she retrieved nanocultures loaded with microbial cells. “Her experiments prove that introducing the cells into the capsules doesn't change the magnetic actuation process,” says Niepa. Usman was able to direct nanoculture movement based on their mass and the strength of the magnetic field.
Real-world simulations demonstrate the broad applications of magnetic nanocultures. Niepa and Usman mixed magnetic and non-magnetic nanocultures to show that their technology can sort separately-encapsulated microbial communities. Targeted retrieval will be key for studies that bring different communities together to observe how they cross-communicate or respond to changes in environmental stressors.
Niepa and Usman also tested how their magnetic nanocultures will function in complex, heterogeneous environments like soil. In separate experiments, they successfully retrieved the magnetic nanocultures from both silica beads and sand samples, with recovery rates as high as 98 percent.
Future work, including field testing, will fine-tune the tool for cultivating and retrieving microorganisms in situ. Versatile and scalable, the technology could be a key to unlocking environmental microbiomes.
This research was supported by the US National Science Foundation under grant DMR-2104731 and by the National Institute of General Medical Sciences of the National Institutes of Health under award number 7DP2GM149553-02. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation or the National Institutes of Health.
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Magnetic nanocultures enable the cultivation and retrieval of elusive microbes.
Artistic depiction of magnetic nanocultures—nanoscale bioreactors encapsulating microorganisms within semi-permeable, iron oxide–functionalized polymer shells—being magnetically actuated toward a magnet. The illustration highlights how these magnetically responsive microenvironments mimic native conditions while enabling targeted recovery of encapsulated microbes from complex ecosystems.
Image credit: Clara Heinrich, Scientific design: animation & illustration — ilustracoescientificas.com.br