Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms
UMass Chan Affiliations
Department of Microbiology and Physiological SystemsProgram in Systems Biology
Document Type
Journal ArticlePublication Date
2020-11-03Keywords
B. subtilisecology
fluorescence microscopy
infectious disease
microbial ecology
microbiology
mucor fragilis
raman microspectroscopy
soil-like microcosms
wet/dry cycles
Environmental Microbiology and Microbial Ecology
Systems Biology
Terrestrial and Aquatic Ecology
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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.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
DOI
10.7554/eLife.56275Permanent Link to this Item
http://hdl.handle.net/20.500.14038/41664PubMed ID
33140722Related Resources
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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.Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.7554/eLife.56275
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Except where otherwise noted, this item's license is described as 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.