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An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
Published on: September 15, 2015
The activity level of a microbial community function can be predicted from its metatranscriptome.
Damian E Helbling1, Martin Ackermann, Kathrin Fenner
1Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
The ISME Journal
|November 19, 2011
Summary
Metatranscriptomics can quantitatively predict biochemical function activity from gene transcript abundance. This predictive capability holds true even for microorganisms comprising as little as 0.05% of a microbial community.
Area of Science:
- Microbiology
- Molecular Biology
- Environmental Science
Background:
- Metatranscriptomics analyzes gene expression in microbial communities.
- Quantitative prediction of microbial function from metatranscriptomics is an active research area.
Purpose of the Study:
- To assess the quantitative predictive power of metatranscriptomics for biochemical function activity.
- To determine the lower limit of microbial abundance for transcript detection and activity prediction.
Main Methods:
- An undefined microbial community was amended with varying amounts of *Escherichia coli* engineered to degrade atrazine.
- The abundance of atrazine-degrading gene transcripts was correlated with the measured transformation activity.
Main Results:
- A linear and proportional relationship was observed between atrazine transformation activity and the abundance of the corresponding gene transcript.
- This relationship was maintained down to an *E. coli* abundance of 0.05% of the total community.
Conclusions:
- Metatranscriptomics offers robust quantitative predictive capabilities for microbial function.
- Transcript abundance is a reliable proxy for enzyme activity, even at low microbial cell densities.
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