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

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.

[1]  Gene W. Tyson,et al.  Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column , 2009, Nature.

[2]  Ming L. Wu,et al.  Nitrite-driven anaerobic methane oxidation by oxygenic bacteria , 2010, Nature.

[3]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[4]  M. Moran,et al.  Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate , 2010, The ISME Journal.

[5]  E. Delong,et al.  Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.

[6]  Anton van Leeuwenhoek.  Environmental Shotgun Sequencing : Its Potential and Challenges for Studying the Hidden World of Microbes , 2007 .

[7]  R. Wolfenden,et al.  The path to the transition state in enzyme reactions: a survey of catalytic efficiencies , 2004 .

[8]  Maureen L. Coleman,et al.  Microbial community gene expression in ocean surface waters , 2008, Proceedings of the National Academy of Sciences.

[9]  E. Delong,et al.  Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea , 2010, Proceedings of the National Academy of Sciences.

[10]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[11]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[12]  L. Wackett,et al.  Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization , 1996, Journal of bacteriology.

[13]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[14]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

[15]  Mary Ann Moran,et al.  Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. , 2009, Environmental microbiology.

[16]  Dmitrij Frishman,et al.  Deciphering the evolution and metabolism of an anammox bacterium from a community genome , 2006, Nature.

[17]  L. Wackett,et al.  Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine , 1995, Applied and environmental microbiology.

[18]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.