Using Shewanella Baltica Ecotypes As A Model For Transcriptional Variation At The Population Level

Abstract

Eukaryotic studies have shown considerable transcriptional variation among individuals of the same population. Owing to the cost of sequencing entire eukaryotic genomes, tested organisms were assumed to be genomically similar or even identical. We overcame this necessary assumption by using four sequenced strains of the bacterium Shewanella baltica, (OS155, OS185, OS195, OS223), as models to assess transcriptional variation and ecotype formation within a prokaryotic population. The strains were isolated from various depths throughout a water column of the Baltic Sea occupying different ecological niches characterized by various abiotic parameters. Although their genome sequences are strikingly similar, when grown in the laboratory under identical conditions, all strains exhibited significantly different growth rates suggesting global expressional variation. To confirm the findings, custom microarray slides containing probes representing all four of the sequenced genomes were hybridized with two strains at a time, in a two color manner, using a loop design. A one way ANOVA designated 415 core genes to be differentially expressed between the four strains at a stringent P value of 0.001. Furthermore, when analyzing common gene sequences shared among 32 other strains within the water column, Ecotype Simulation software consistently grouped all four model strains into discrete ecotypes. Transcriptional pattern variations such as the ones highlighted here may be used as indicators of short-term evolution emerging from the formation of bacterial ecotypes.