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Effects of genetically modified potatoes with increased zeaxanthin content on the abundance and diversity of rhizobacteria with in vitro antagonistic activity do not exceed natural variability among cultivars

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Abstract

To assess potential effects of genetically modified (GM) potatoes on the abundance and diversity of rhizobacteria with in vitro antagonistic activity in relation to natural variability among cultivars, two GM potato lines accumulating the carotenoid zeaxanthin in their tubers, the parental cultivar and four additional commercial cultivars were planted at two field sites in Germany. Rhizosphere samples were taken at three developmental stages of the plants. A total of 3,985 bacteria isolated from the rhizosphere were screened for their in vitro antagonistic activity towards Rhizoctonia solani, Verticillium dahliae and Phytophthora infestans using a dual-culture assay. Genotypic characterisation, 16S rRNA gene sequencing and antifungal metabolite analysis was performed to characterize the 595 antagonists obtained. The 16S rRNA gene-based identification of in vitro antagonists revealed strong site-dependent differences in their taxonomic composition. This study showed that the site was the overriding factor determining the proportion and diversity of antagonists from the rhizosphere of potato while the effect of the genetic modification on the proportion of antagonists obtained did not exceed natural variability among the five commercial cultivars tested.

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Acknowledgements

This work was funded by grant 0313277B from the Bundesministerium für Bildung und Forschung. The authors thank U. Zimmerling, A. Büttner and G. Czeplie for valuable assistance in the lab and Dr. F. Niepold for providing the P. infestans isolate. We thank Dr. Holger Heuer and Dr. Siegfried Kropf for discussion in statistical questions. I.-M. Jungkurth is gratefully acknowledged for reading the manuscript. The authors would like to thank J. Dennert and F.X. Maidl (Technical University of Munich) for the perfect management of the experimental plots in Roggenstein and Oberviehhausen. The authors are highly thankful to G. Wenzel (Technical University of Munich) for providing the plant material of the transgenic lines.

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  1. Julius Kühn-Institute - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg, 11–12, 38104 Braunschweig, Germany

    Nicole Weinert, Christine Gottwald & Kornelia Smalla

  2. Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010, Graz, Austria

    Remo Meincke & Gabriele Berg

  3. Department for Terrestrial Ecogenetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85758, Oberschleissheim, Germany

    Viviane Radl & Michael Schloter

  4. Technical University of Munich, Chair for Plant Breeding, Am Hochanger 4, 85350, Freising, Germany

    Xia Dong

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Correspondence to Kornelia Smalla.

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Fig. S1

BOX-PCR fingerprints of in vitro antagonists identified as Pseudomonas fluorescens isolated from the potato rhizospheres in Roggenstein (A) and Oberviehhausen (B), respectively. ST = Standard (1 Kb Plus DNA Ladder). Strain code: cultivar/GM line (Bal = ‘Baltica’; SR47 = ‘Baltica’ co-suppression; SR48 = ‘Baltica’ antisense; Sel = ‘Selma’; Des = ‘Désirée’; Dit = ‘Ditta’; Sib = ‘Sibu’), sampling time (2 = EC60, 3 = EC90), number of replicate plot analysed (1 to 4). * of isolates that were obtained two times from the same plot and showed identical BOX patterns only one representative isolate is shown. (DOC 1,344 kb)

Fig. S2

BOX-PCR profiles of in vitro antagonists identified as Bacillus pumilus isolated from the potato rhizospheres in Roggenstein and Oberviehhausen, respectively. (A) BOX-profiles of a subset of isolates from the potato rhizosphere in Roggenstein. (B) BOX-profiles displayed by the majority of isolates (68/80) identified as Bacillus pumilus isolated from the potato rhizosphere in Oberviehhausen. ST = Standard (1 Kb Plus DNA Ladder). Strain code: cultivar/GM line (Bal = ‘Baltica’; SR47 = ‘Baltica’ co-suppression; SR48 = ‘Baltica’ antisense; Sel = ‘Selma’; Des = ‘Désirée’; Dit = ‘Ditta’; Sib = ‘Sibu’); sampling time (2 = EC60, 3 = EC90), number of replicate plot analysed (1 to 4). * of isolates that were obtained several times from the same plot and showed identical BOX patterns only one representative isolate is shown. (DOC 1,275 kb)

Fig. S3

BOX-profiles of isolates identified as Pectobacterium chrysanthemi (lanes 2–11), P. carotovorum (lanes 12–14) and P. atrosepticum (lane 15) from the potato rhizospheres in Roggenstein (R) and Oberviehhausen (O), respectively. ST = Standard (1 Kb Plus DNA Ladder). Strain code: cultivar/GM line (SR47 = ‘Baltica’ co-suppression; SR48 = ‘Baltica’ antisense; Des = ‘Désirée’; Dit = ‘Ditta’), sampling time (2 = EC60, 3 = EC90), number of replicate plot analysed (1 to 4). * of isolates that were obtained several times from the same plot and showed identical BOX patterns only one representative isolate is shown. (DOC 892 kb)

Table S1

Proportions of in vitro antagonistic isolates in the potato rhizospheres of the sampling site in Roggenstein (A) and Oberviehhausen (B) towards Rhizoctonia solani AG3, Verticillium dahliae ELV25 and Phytophthora infestans as determined by dual-culture assays. (DOC 93 kb)

Table S2

Phylogenetic affiliation of identified in vitro antagonists from both sampling sites determined by partial 16S rRNA gene sequence analysis. Numbers in parenthesis indicate the numbers of isolates that were identified based on the same BOX-fingerprint (>85% similarity). Rog = Roggenstein, Ovh = Oberviehhhausen; EC60 = flowering plants, EC90 = senescent plants; Bal = ‘Baltica’, SR47 = ‘Baltica’ co-suppression, SR48 = ‘Baltica’ antisense, Sel = ‘Selma’, Des = ‘Désirée’, Dit = ‘Ditta’, Sib = ‘Sibu’. Numbers following the cultivar/GM line indicate the plot (1 to 4). (DOC 1,098 kb)

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Weinert, N., Meincke, R., Gottwald, C. et al. Effects of genetically modified potatoes with increased zeaxanthin content on the abundance and diversity of rhizobacteria with in vitro antagonistic activity do not exceed natural variability among cultivars. Plant Soil 326, 437–452 (2010). https://doi.org/10.1007/s11104-009-0024-z

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