The activity level of a microbial community function can be predicted from its metatranscriptome

ISME J. 2012 Apr;6(4):902-4. doi: 10.1038/ismej.2011.158. Epub 2011 Nov 17.


The objective of this work was to improve our understanding of the quantitative predictive capabilities of metatranscriptomics. To meet this objective, we investigated whether we can predict the activity level of a specific biochemical function based on the abundance of the corresponding gene transcript within measured community metatranscriptomes. In addition, we investigated the lower limit of a microorganism's abundance that still allows detection of its transcripts within a metatranscriptome and prediction of the activity levels of the enzyme encoded by the transcript. To do this, we amended an undefined microbial community with varying fractions of an Escherichia coli strain that can catalyze a specific transformation reaction for the herbicide atrazine. We observed a linear and proportional relationship between the activity level of the transformation reaction and the abundance of its associated encoding transcript down to an E. coli cell density of 0.05% of the population.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Atrazine / pharmacology
  • Escherichia coli / drug effects
  • Escherichia coli / enzymology
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism*
  • Gene Expression Profiling / methods*
  • Herbicides / pharmacology
  • Hydrolases / genetics
  • Hydrolases / metabolism
  • Metagenomics / methods*


  • Herbicides
  • Hydrolases
  • atrazine chlorohydrolase
  • Atrazine