Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes.

Microbial Informatics and Experimentation
Ivaylo KostadinovFrank Oliver Glöckner

Abstract

DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated. We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool. Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagen...Continue Reading

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Citations

Mar 16, 2012·FEMS Microbiology Ecology·Pelin YilmazFrank O Glöckner

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Methods Mentioned

BETA
environmental stress

Software Mentioned

R
MegDb
transeq
vegan
EMBOSS package
MASS
Rcode
HMMER3
megx
net

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