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Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings


Background and aims

Forest ecosystems may act as sinks for or source of atmospheric CO2. While inorganic nitrogen (N) fertilization increases aboveground tree biomass, the effects on soil and rhizosphere microorganisms are less clear, indicating potentially unpredictable changes in nutrient cycling processes maintaining ecosystem functioning. Although plant-derived carbon (C) is the main C source in soils during the vegetation period, information on the response of rhizosphere bacteria assimilating rhizodeposits to increased soil N availability mainly for trees is missing.


We performed a greenhouse experiment with 13C-CO2 labelled young beech seedlings grown under different N fertilization levels. DNA Stable Isotope Probing (DNA-SIP) in combination with TRFLP and pyrosequencing enabled us to identify bacteria assimilating plant-derived C and to assess the main responders phylogenetically.


Although above- and belowground allocation of recently fixed photosynthates remained unchanged, microbial rhizosphere community composition was clearly affected by fertilization. Besides, we found lower 13C incorporation into microbial biomass in fertilized soil. Moreover, it could be shown that only a small subset of the rhizosphere microbiome incorporated recently fixed C into its DNA, dominated by Proteobacteria (Alpha- and Betaproteobacteria) and Actinobacteria (Actinomycetales).


Our results suggest that N fertilization may change both the diversity of bacterial communities using rhizodeposits and assimilation rates of recently fixed photosynthates. Given the close interaction of beneficial and/or deleterious microbes and plants in the rhizosphere, this could potentially have positive or negative implications for plant performance on long-term.

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We gratefully acknowledge Susanne Kublik and Kornelia Galonska for their assistance in molecular analysis.

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Correspondence to Silvia Gschwendtner.

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Responsible Editor: Liesje Mommer.

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Abundance of 16S rRNA genes ng-1 DNA among 10 gradient fractions of DNA extracted from (a) unfertilized and (b) fertilized soils after 2, 4, 7 and 10 days of growth in 13C-CO2 labelled and unlabeled atmosphere quantified via real-time PCR (n = 1). (GIF 48 kb)

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UPGMA dendrogram generated from TRFLP profiles based on 16S rRNA gene amplicons from 12 gradient fractions (numbered 1–12) of DNA extracted from (a) unfertilized (4 days) and (b) fertilized (7 days) soils obtained from unlabeled (C12) and labelled (C13) pots (n = 3). Buoyant density of the gradient fractions increased with decreasing fraction number. The scale indicates the distance level. (GIF 52 kb)

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Rarefaction curves of partial 16S rRNA gene sequences after DNA extraction and PCR amplification obtained from heavy (h) and medium (m) fractions from unfertilized (f0, 4 days) and fertilized (f10, 7 days) soils and unlabeled (C12) and labelled (C13) pots at 97 % similarity level normalized with respect to sample size (n = 1). (GIF 66 kb)

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(PDF 125 kb)


Phylogenetic dendrogram (maximum likelihood consensus tree) showing the distribution of sequences related to (a) Proteobacteria and (b) Actinobacteria derived from unfertilized and fertilized rhizosphere soil after 4 and 7 days of incubation, respectively. OTUs representing bacteria assimilating plant-derived C are highlighted in grey. (GIF 132 kb)

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Gschwendtner, S., Engel, M., Lueders, T. et al. Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings. Plant Soil 407, 203–215 (2016).

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  • Fertilization
  • Plant-derived carbon
  • Rhizosphere microbiome
  • Pyrosequencing