Thermal transcriptome of Synechococcus in response to acute and chronic thermal stress

Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the marine cyanobacteria species Synechoccocus. The dataseries was composed of two experiments; (i) "Steady State" experiment designed to characterised the acclimated (balanced-growth) transcriptomic response to sub- and supra-optimal temperatures (i.e., chronic thermal stress), and (ii) a "Ramp" experiment designed to characterise the transient changes in the transcriptome in response to gradual increase in temperature (i.e., acute thermal stress). Overall design: For "Steady State" experiments, cultures (n=4) were grown for more than 10 generations at three temperatures (20, 27 and 31.5 C). Cells were harvested in exponential growth phase by filtering at least 50 mL on to a polycarbonate membrane and flash freezing in liquid nitrogen. Cultures grown at 27 C (thermal optimal) were used as a reference transcriptome. For "Ramp" experiment, Synechococcus sp. was grown for more than 10 generations at optimal temperature conditions of 27 C using semi-continuous culture methods. During exponential phase, an inoculum was used to seed individual experimental vessels (n=4), also maintained at 27 C, the temperature of which was regulated (+-0.5 C) using a custom-built glass water-jacket. Cultures were stirred and gassed with sterile lab air to remove build-up of oxygen at high cell abundances. The cell abundances of each experimental vessel was monitored through time and once cell densities had reached 5x10^6 cells mL-1, approximately 5 generations following inoculation, a batch-fed culturing system was initiated whereby the dilution rate was set by the daily growth rate over the previous 24 h interval. At this time, a volume of culture was removed and sampled for physiology and transcriptomics before being replaced by the same volume of fresh, thermostatted medium. Following sample harvest, the temperature was increased stepwise stepwise (1 C d-1) at the same time of day for 5 days, from thermal conditions approximating the strains optima (27 C) to a maximum temperature of 32 C. The first timepoint (Timepoint = 0), where cultures were grown at 27 C, were used as a reference transcriptome.