E-GEOD-54814 - Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand [experiment 1]

Released on 23 June 2014, last updated on 30 June 2014
Sphingomonas wittichii RW1
Samples (18)
Array (1)
Protocols (8)
The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.
Experiment type
transcription profiling by array 
Silvia K. Moreno-Forero <silvia.moreno@unil.ch>, Jan R van der Meer, Silvia K Moreno-Forero
Investigation descriptionE-GEOD-54814.idf.txt
Sample and data relationshipE-GEOD-54814.sdrf.txt
Raw data (1)E-GEOD-54814.raw.1.zip
Processed data (1)E-GEOD-54814.processed.1.zip
Array designA-GEOD-15452.adf.txt