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

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.