title: DNA-based stable isotope probing enables the identification of active bacterial endophytes in potatoes.
abstract: A (13)CO2 (99 atom-%, 350 ppm) incubation experiment was performed to identify active bacterial endophytes in two cultivars of Solanum tuberosum, cultivars Desirée and Merkur. We showed that after the assimilation and photosynthetic transformation of (13)CO2 into (13)C-labeled metabolites by the plant, the most directly active, cultivar specific heterotrophic endophytic bacteria that consume these labeled metabolite scan be identified by DNA stable isotope probing (DNA-SIP).Density-resolved DNA fractions obtained from SIP were subjected to 16S rRNA gene-based community analysis using terminal restriction fragment length polymorphism analysis and sequencing of generated gene libraries.Community profiling revealed community compositions that were dominated by plant chloroplast and mitochondrial 16S rRNA genes for the 'light' fractions of (13)CO2-incubated potato cultivars and of potato cultivars not incubated with (13)CO2. In the 'heavy' fractions of the (13)CO2-incubated endophyte DNA, a bacterial 492-bp terminal restriction fragment became abundant, which could be clearly identified as Acinetobacter and Acidovorax spp. in cultivars Merkur and Desirée,respectively, indicating cultivar-dependent distinctions in (13)C-label flow. These two species represent two common potato endophytes with known plant-beneficial activities.The approach demonstrated the successful detection of active bacterial endophytes in potato. DNA-SIP therefore offers new opportunities for exploring the complex nature of plant-microbe interactions and plant-dependent microbial metabolisms within the endosphere.
authors.affiliation: Austrian Research Centers GmbH, Department of Bioresources, A-2444 Seibersdorf, Austria.|Present address: University of Hohenheim, Institute for Plant Production and Agroecology in the Tropics and Subtropics, D-70593 Stuttgart, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Rasche
authors.affiliation: Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Groundwater Ecology, D-85764 Neuherberg, Germany.
authors.forename: Tillmann
authors.initials: T
authors.lastname: Lueders
authors.affiliation: Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
authors.affiliation: Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Groundwater Ecology, D-85764 Neuherberg, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Schaefer
authors.affiliation: Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
authors.forename: Franz
authors.initials: F
authors.lastname: Buegger
authors.affiliation: Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gattinger
authors.affiliation: FAO/IAEA Agriculture and Biotechnology Laboratory, A-2444 Seibersdorf, Austria.
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Hood-Nowotny
authors.affiliation: Austrian Research Centers GmbH, Department of Bioresources, A-2444 Seibersdorf, Austria.
authors.forename: Angela
authors.initials: A
authors.lastname: Sessitsch
mesh_terms: D000150:Acinetobacter / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D002245:Carbon Dioxide / Q000737:chemistry; D002247:Carbon Isotopes; D042621:Comamonadaceae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000737:chemistry; D015723:Gene Library; D015336:Molecular Probe Techniques; D012150:Polymorphism, Restriction Fragment Length; D012329:RNA, Bacterial / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000382:microbiology*
chemical_list: D002247:Carbon Isotopes; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D002245:Carbon Dioxide