Microfluidic chips provide visual access to in situ soil ecology

Paola Micaela Mafla-Endara,Pelle Ohlsson,Milda Pucetaite,Carlos Arellano-Caicedo,Edith C Hammer,Kristin Aleklett

doi:10.1038/s42003-021-02379-5

Paola Micaela Mafla-Endara, Pelle Ohlsson + Show 4 more

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https://doi.org/10.1038/s42003-021-02379-5

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Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent ‘soil chips’ with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae (‘fungal highways’) strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.

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Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish
The system is highly dynamic in space and time: solid particles are moved by both physical processes and biota, and additional barriers for diffusion and mass flow occur when pores dry out, inhibiting the dispersal of microorganisms such as bacteria and protists that are reliant on hydraulic connectivity for relocation[9,10,11]
Even within soil science and microbial ecology, chips have been used to address important questions[21,22] such as how to increase the number of culturable bacteria from the environment[23], how bacteria spatially organize in a pore space along chemical gradients[24], and how intracellular signals propagate in fungal networks[25]

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Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Transparent ‘soil chips’ with soil, or bury them directly in the field Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as interkingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae (‘fungal highways’) strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets Physical forces such as water movements, and organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We studied the early microbial colonization of the chip’s pristine, soil-like habitat by (I) burying it directly into the soil habitat in the field, or (II)

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