title: Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce.
abstract: Bacterial biocontrol strains used as an alternative to chemical fungicides may influence bacterial communities in the rhizosphere and effects might differ depending on the soil type. Here we present baseline data on the effects of Pseudomonas jessenii RU47 on the bacterial community composition in the rhizosphere of lettuce grown in diluvial sand, alluvial loam and loess loam at the same field site. 16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. DGGE fingerprints revealed that in three consecutive years (2010-2012) RU47 had a slight but statistically significant effect on the bacterial community composition in one (2010), two (2011) or all the three soils (2012). However, these effects were much less pronounced compared with the influence of soil types. Additional pyrosequence analysis of samples from 2011 showed that significant changes in bacterial community compositions in response to RU47 inoculation occurred only in alluvial loam. Different taxonomic groups responded to the RU47 application depending on the soil type. Most remarkable was the increased relative abundance of OTUs belonging to the genera Bacillus and Paenibacillus in alluvial loam. Pyrosequencing allowed side-effects of the application of bacterial inoculants into the rhizosphere to be identified.
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; Department Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V., Großbeeren, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Schreiter
authors.forename: Guo-Chun
authors.initials: GC
authors.lastname: Ding
authors.forename: Rita
authors.initials: R
authors.lastname: Grosch
authors.forename: Siegfried
authors.initials: S
authors.lastname: Kropf
authors.forename: Kai
authors.initials: K
authors.lastname: Antweiler
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D061271:Acidobacteria / Q000145:classification / Q000235:genetics; D039903:Actinobacteria / Q000145:classification / Q000235:genetics; D059827:Agricultural Inoculants / Q000145:classification* / Q000235:genetics; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics; D001483:Base Sequence; D058645:Denaturing Gradient Gel Electrophoresis; D018545:Lactuca / Q000235:genetics / Q000382:microbiology*; D059013:Microbial Consortia; D018517:Plant Roots / Q000382:microbiology*; D020560:Proteobacteria / Q000145:classification / Q000235:genetics; D011549:Pseudomonas / Q000502:physiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012987:Soil / Q000145:classification; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D012987:Soil
keywords: 16S rRNA gene; Pseudomonas jesseniiRU47; biocontrol; denaturing gradient gel electrophoresis; pyrosequencing; total community DNA