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. 2014 Apr 17;10(4):e1004283.
doi: 10.1371/journal.pgen.1004283. eCollection 2014 Apr.

A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota

Natacha Bodenhausen  1 , Miriam Bortfeld-Miller  1 , Martin Ackermann  2 , Julia A Vorholt  1
Affiliations

A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota

Natacha Bodenhausen et al. PLoS Genet. .

Abstract

The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Experimental strategy to identify the plant genes responsible for changes in community composition and/or total bacterial abundance.
See text for details.
Figure 2
Figure 2. Different A. thaliana plant genotypes (55 in total) were tested for changes in bacterial community composition and abundance in independent experiments.
(a) Results of the ARISA analysis. The average Bray-Curtis index was calculated for each genotype compared to the wild-type in pairwise comparisons and divided by the average Bray-Curtis index for each genotype with itself (see Figure S7 for individual values). Col-0 was used to normalize for most genotypes, except for mutants with a different background, which were normalized to their respective background. The horizontal dashed line indicates the limit of reproducibility of the system, mutants very close to this threshold could either be confirmed (Figure 3) or not (Figure S8). (b) Results of the qPCR analysis. The up and down bars indicate higher and lower 16S rRNA gene copy numbers, respectively, compared to the wild-type Col-0 samples (Bonferroni-adjusted P value <0.05). For each genotype there were 3–4 DNA pools from five plants. The same DNA extracts were used for ARISA and qPCR analysis.
Figure 3
Figure 3. Different community compositions were detected on the cuticle and ethylene mutants.
(a) Cuticle mutants (b) Defense signaling mutants. Average (± s.e.m) relative fluorescence intensity (RFI). Asterisks indicate a significant plant genotype effect for the RFI of the bacterial species (*, P<0.05; **, P<0.01, ***, P<0.001; Bonferroni-adjusted P values). Letters indicate a significant effect of the genotype compared to Col-0 (P<0.05, Dunnet's test). There were four (a) and six (b) DNA pools from five plants for each genotype. These experiments were repeated at least in triplicate with similar results. Bacterial species abbreviations: Arthrobacter = Arthrobacter sp. #968, MetPA1 = Methylobacterium extorquens PA1, Mradio = Methylobacterium radiotolerans 0-1T, Rhodoccus = Rhodococcus sp., SphFR1 = Sphingomonas sp. Fr1, Sphyllo = Sphingomonas phyllosphaerae, Vario = Variovorax sp.
Figure 4
Figure 4. Higher 16S rRNA gene copy numbers were found for the lacs2 mutant compared to the wild-type plants.
The number of 16S rRNA gene copies was normalized using a plant gene AT4G33380 and normalized to the wild-type. The number of DNA pools analyzed for each genotype is indicated in the barplot. Asterisks indicate a significant effect for genotype compared to Col-0 (*, P<0.05; **, P<0.01; Student's t-test, Bonferroni- adjusted P values). These experiments were repeated at least in triplicate with similar results.
Figure 5
Figure 5. Natural variation in the host has an effect on its associated bacterial communities.
(a) Community composition determined by ARISA. Average relative fluorescence intensity (± s.e.m). For abbreviations see Figure 3. Letters indicate a significant effect of the genotype compared to Col-0 (P<0.05, Dunnet's test). (b) 16S rRNA gene copy number. Asterisks indicate a significant effect of genotype compared to Col-0 (*, P<0.05; **, P<0.01; ***, P<0.001; Bonferroni-adjusted P values). There were 6 DNA pools from five plants for each genotype. These experiments were repeated in triplicate with similar results.
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References

    1. Vorholt JA (2012) Microbial life in the phyllosphere. Nature Rev Microbiol 10: 828–840. - PubMed
    1. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17: 478–486. - PubMed
    1. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84: 11–18. - PubMed
    1. Conrath U, Beckers GJ, Flors V, Garcia-Agustin P, Jakab G, et al. (2006) Priming: getting ready for battle. Mol Plant Microbe Interact 19: 1062–1071. - PubMed
    1. Pieterse CM, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28: 489–521. - PubMed

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This work was supported by the Swiss National Science Foundation (Marie Heim-Vögtlin Grant to NB) and ETH Zurich. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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