DNA-based stable isotope probing enables the identification of active bacterial endophytes in potatoes.
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.
Rasche
Frank
F
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.
Lueders
Tillmann
T
Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Groundwater Ecology, D-85764 Neuherberg, Germany.
Schloter
Michael
M
Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
Schaefer
Sabine
S
Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Groundwater Ecology, D-85764 Neuherberg, Germany.
Buegger
Franz
F
Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
Gattinger
Andreas
A
Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Soil Ecology, D-85764 Neuherberg, Germany.
Hood-Nowotny
Rebecca C
RC
FAO/IAEA Agriculture and Biotechnology Laboratory, A-2444 Seibersdorf, Austria.
Sessitsch
Angela
A
Austrian Research Centers GmbH, Department of Bioresources, A-2444 Seibersdorf, Austria.
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*
D002247:Carbon Isotopes; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D002245:Carbon Dioxide