Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment
Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible.
- Research Organization:
- Montana State Univ., Bozeman, MT (United States)
- Sponsoring Organization:
- USDOE; National Science Foundation (NSF); National Aeronautics and Space Administration (NASA); W. M. Keck Foundation; Gordon and Betty Moore Foundation (GBMF); Montana State University
- Grant/Contract Number:
- DBI-1736255; 80NSSC19K1633; 80NSSC19K0449; GBMF5999
- OSTI ID:
- 1816836
- Journal Information:
- The ISME Journal, Vol. 14, Issue 11; ISSN 1751-7362
- Publisher:
- Nature Publishing GroupCopyright Statement
- Country of Publication:
- United States
- Language:
- English
From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology
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journal | October 2020 |
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