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Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Citation

Shank, Elizabeth et al. (2021), Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms, Dryad, Dataset, https://doi.org/10.5061/dryad.41ns1rnb3

Abstract

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

Methods

These data include Raman spectra and confocal fluorescence images.

Funding

Biological and Environmental Research, Award: DE-SC0013887

Biological and Environmental Research, Award: DE-SC0019012

European Research Council, Award: FunKeyGut 741623