To characterize the microbial communities in potato tuber, we used potatoes harvested in 2012 (Experiment 1) and 2013 (Experiment 2). Experiment 1 was performed using potato tubers that were stored until March 2013 while Experiment 2 was performed using tubers stored until December 2013. Because of this time difference we expected that the results of these experiments would differ while preserving some common features that could be interpreted as reflecting general aspects of changes in the potato microbiome in response to infection with Pectobacterium atrosepticum SCRI1043.
Every potato tuber was infected with the minimum number of P. atrosepticum cells (1.5 × 104 cells per ml) required to induce maceration (as determined by preliminary experiments). In Experiment 1, we sampled the macerated tissue from potato tubers incubated for either two, five, or eight days after infection with P. atrosepticum. The fifth day of sampling was not performed in Experiment 2 because the bacterial counts determined in Experiment 1 for the fifth and eighth day samples were quite similar. Figure 1 provides an overview of the experimental setup.