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Does inoculation with Pseudomonas fluorescens LBUM223 impact the rhizosphere and geocaulosphere microbiomes of potato?

Amy Novinscak: Université de Moncton

<div>The phenazine-1-carboxylic acid (PCA)-producing <em>Pseudomonas fluorescens</em> strain LBUM223 shows biocontrol potential against <em>Streptomyces scabies</em>, causing common scab of potato. To better characterize the impact of inoculating a specific biocontrol agent under natural field conditions, the microbiomes of the rhizosphere and the geocaulosphere of potato plants were characterized using Next-Gen sequencing. One initial or bi-weekly applications of LBUM223 were performed up to 11 weeks after planting (in addition to non-inoculated plants). Rhizosphere and geocaulosphere (when potato tubers were produced) soils were sampled every two weeks. Following soil DNA extractions, 16S rRNA gene amplification and sequencing was performed using the Illumina MiSeq technology. The QIIME pipeline was used for data analyses. Results were generated from 45 rhizosphere and 27 geocaulosphere samples, for which 63 502 and 44 469 different operational taxonomical units were observed. Diversity comparisons between both datasets were performed. To our knowledge, it is the first time that the geocaulosphere microbiome is characterized and compared to the rhizosphere. 11 phyla accounted for 95% of the diversity, with <em>Actinobacteria</em>, <em>Proteobacteria</em>, <em>Chloroflexi</em> and <em>Acidobacteria</em> being the most important ones. Overall, the results obtained suggest that <em>Pseudomonas fluorescens</em> LBUM223 does not significantly interfere with the autochthonous rhizosphere nor geocaulosphere microbiomes.</div>