Microfluidic Chips to Monitor Microbial Cities within In Situ Soil Ecosystems

August 3, 2021. By Kolemann Lutz

Researchers in Sweden tested and analysed hundreds of paths of microorganisms on microfluidic soil chips to evaluate the inter-kingdom and food-web interactions, as well as the architecture, engineering, and optimisation of vast underground microbial cities. Trend detection algorithms can be applied to microscopic soil data in various spectral bands to determine the efficacy of hyphae (‘fungal highways') growth, soil pore space architecture, water flow, nutrient intake and distribution, bioremediation, and colonisation of microorganisms with the potential to evaluate how well soil microorganisms (bacteria, fungi, protists) and invertebrates are adapting and performing in lunar and Martian environments.

A subterranean kingdom of fungi, flagellates(protozoan bacteria), and free-living amoebae (FLA) live in a vast microbial world in the soil beneath our feet. Around 1600 species of protozoan bacteria have been recorded from soil on Earth, many of which have special adaptations to the soil environment. As settler’s transition to cultivating crops with the soil on the surface, it is important to monitor the microbial adaptations and interactions in the Martian environment.

By scooping samples for lab studies, soil microbial ecosystems often become destroyed after moving the delicate structures of mud, water, and air in which the soil microbes reside. As a result, soil science has been limited, including the impact of spatial microstructures on biogeochemical processes like nutrient cycling, feedbacks between microbes and soil physical processes, inter-kingdom interactions, and biodiversity-function relationships.

What if it was possible to spy on these underground organisms and dwellers, who recycle organic matter, without disturbing their micro-habitats?

Microfluidic chips have already demonstrated their usefulness in controlling and shaping micro-environments for the study of cell-to-cell interactions, and revolutionized biomedical research with, e.g., organ-on-a-chip devices. This soil-on-a-chip technology can also house soil microbial groups and has already contributed significantly to the study of bacteria, nematodes, fungi and plants, as well as inter-organismal interactions.

Chips have been used to passively monitor and address important question such as how to increase the number of culturable bacteria from the environment, how bacteria spatially organize in a pore space along chemical gradients, and how intracellular signals propagate in fungal networks.

Swedish Researchers from Lund University and others developed a new kind of "cyborg soil", which is half natural and half artificial, to investigate interactions within multi-species microbial communities on the microengineered chips buried in the wild or with soil in the lab. With the transparent air-filled chip cut to mimic the pore structures of natural soil, scientists aimed to address how microbial dispersal is influenced by soil pore spaces, the impact of pore space geometry and channels, the impact of dry and wet soils on moving and growing microorganisms, as well as the spatial arrangement of chip pore spaces.

Several hundred possible paths were analysed on the soil chips, including several thousand individual pore spaces, with Raman scattering microspectroscopy. Images extracted and analyzed from 22 videos published open access in a research paper in July 2021 in the Communications Biology Journal.

As resting bacteria get pushed around by the movement of water molecules, water clings to surfaces. Additionally, soil particle velocity in water flow paths was analysed. Researchers noted that soil air bubbles form insurmountable barriers for many microorganisms primarily because of the surface tension of the water around them. The experiments demonstrate that H2O and nutrient conditions mainly affect water-dwelling organism groups of bacteria and protists. Spatial microscopy data indicated that water movements and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals.

Fungal hyphae, which burrow like plant roots underground, quickly grew throughout the cyborg soil pores, forming "fungal highways" along which bacteria "hitchhike" to disperse through soil, a phenomenon known only from lab studies. With their strong hyphal tips, fungi often act like "ecosystem engineers", opening up passages and blocking others with their cells to build many of the long term micro transportation infrastructure such as the streets, avenues, and bridges in the microbial metropolis.

Researchers noted that the shape of the soil microstructures has an effect on fungal dispersal. Fungal hyphae strongly enhance the colonization ability for both bacteria and diverse unicellular protists in an initially dry pore space via increased pore wetting. The chips also reveal spatiotemporal changes of microhabitats: hyphae both open up new passages in the pore spaces and block avenues for both organisms and abiotic soil components.

The experiment found that hyphae are an important vector for the dispersal of a large variety of swimming microorganisms, in addition to a high number of single celled protists that ride on the fungal highway, a so-far completely unexplored phenomenon.

Microengineered chips hold great potential to monitor the biological adaptation to life in 3/8Gs and 44% solar irradiance on the Martian surface.

All major groups of soil microorganisms (bacteria, fungi, protists), as well as invertebrates such as nematodes and microarthropods, can be analyzed at the microscopic level to determine the efficacy of soil pore space architecture, water flow, nutrient intake and distribution, bioremediation, and colonisation of microorganisms.

Upon the creation of long term fungal highways and traffic infrastructure, a network of underground spatial microchips can help monitor the effectives of 3/8's gravity and sunlight-induced differences on single celled oil-city dwellers and fungal architectures in bioremediated Martian and Lunar soils. Additional studies may investigate improving the design, engineering, and material properties of microfluidic chips perhaps to become biodegradable with greater spectral data scenes.

Further research is required to isolate variables and study how microbial worlds influence major C3 crops on Earth and in extreme environments, which holds potential to help guide desirable or less desirable genetic traits and inform software systems to engineer life on new worlds.


Mafla-Endara, P.M., Arellano-Caicedo, C., Aleklett, K. et al. Microfluidic chips provide visual access to in situ soil ecology. Commun Biol 4, 889 (2021). https://doi.org/10.1038/s42003-021-02379-5

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