Different Selective Effects on Rhizosphere Bacteria Exerted by Genetically Modified versus Conventional Potato Lines

<div><p>Background</p><p>In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with ¹³C-CO₂ and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released ¹³C labelled carbonaceous compounds.</p><p>Methodology/Principal findings</p><p>The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released ¹³C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera <i>Pseudomonas</i> and <i>Burkholderia,</i> were strong accumulators of the ¹³C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus <i>Pseudomonas,</i> next to <i>Gluconacetobacter</i> and <i>Paracoccus</i>. Cultivar Modena mainly attracted <i>Burkholderia</i>, next to <i>Moraxella</i>-like (Moraxellaceae family) and <i>Sphingomonas</i> types.</p><p>Conclusions/Significance</p><p>Based on the use of <i>Pseudomonas</i> and <i>Burkholderia</i> as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.</p>