title: Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines.
abstract: BACKGROUND
  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 (13)C-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 (13)C labelled carbonaceous compounds.
  
  
  RESULTS
  The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-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 Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.
  
  
  CONCLUSIONS
  Based on the use of Pseudomonas and Burkholderia 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.
authors.affiliation: Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, RUG, Groningen, The Netherlands.
authors.forename: Armando Cavalcante Franco
authors.initials: AC
authors.lastname: Dias
authors.forename: Francisco
authors.initials: F
authors.lastname: Dini-Andreote
authors.forename: Silja Emilia
authors.initials: SE
authors.lastname: Hannula
authors.forename: Fernando Dini
authors.initials: FD
authors.lastname: Andreote
authors.forename: Michele de Cássia
authors.initials: Mde C
authors.lastname: Pereira E Silva
authors.forename: Joana Falcão
authors.initials: JF
authors.lastname: Salles
authors.forename: Wietse
authors.initials: W
authors.lastname: de Boer
authors.forename: Johannes
authors.initials: J
authors.lastname: van Veen
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D044822:Biodiversity; D015415:Biomarkers / Q000378:metabolism; D005227:Fatty Acids / Q000737:chemistry / Q000378:metabolism; D054892:Metagenome; D064307:Microbiota; D010641:Phenotype; D010743:Phospholipids / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D030821:Plants, Genetically Modified; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D012988:Soil Microbiology; D011198:Solanum tuberosum / Q000235:genetics / Q000254:growth & development / Q000382:microbiology*
chemical_list: D015415:Biomarkers; D005227:Fatty Acids; D010743:Phospholipids; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S