UMMS Affiliation

Program in Systems Biology; Department of Microbiology and Physiological Systems

Publication Date

2020-11-03

Document Type

Article

Disciplines

Environmental Microbiology and Microbial Ecology | Systems Biology | Terrestrial and Aquatic Ecology

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.

Keywords

B. subtilis, ecology, fluorescence microscopy, infectious disease, microbial ecology, microbiology, mucor fragilis, raman microspectroscopy, soil-like microcosms, wet/dry cycles

Rights and Permissions

Copyright Sharma et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

DOI of Published Version

10.7554/eLife.56275

Source

Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. Elife. 2020 Nov 3;9:e56275. doi: 10.7554/eLife.56275. PMID: 33140722; PMCID: PMC7609051. Link to article on publisher's site

Journal/Book/Conference Title

eLife

Related Resources

Link to Article in PubMed

PubMed ID

33140722

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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