Rhizosphere microorganisms can influence the timing of plant flowering

Abstract

Background: Plant phenology has crucial biological, physical, and chemical effects on the biosphere. Phenological drivers have largely been studied, but the role of plant microbiota, particularly rhizosphere microbiota, has not been considered.

Results: We discovered that rhizosphere microbial communities could modulate the timing of flowering of Arabidopsis thaliana. Rhizosphere microorganisms that increased and prolonged N bioavailability by nitrification delayed flowering by converting tryptophan to the phytohormone indole acetic acid (IAA), thus downregulating genes that trigger flowering, and stimulating further plant growth. The addition of IAA to hydroponic cultures confirmed this metabolic network.

Conclusions: We document a novel metabolic network in which soil microbiota influenced plant flowering time, thus shedding light on the key role of soil microbiota on plant functioning. This opens up multiple opportunities for application, from helping to mitigate some of the effects of climate change and environmental stress on plants (e.g. abnormal temperature variation, drought, salinity) to manipulating plant characteristics using microbial inocula to increase crop potential.

Keywords: Arabidopsis; Flowering time; Indole acetic acid; Microbiota; Nitrogen; Rhizosphere; Root exudate.

Fig. 1

Design of the microcosmic experiment across generations and the profiles of rhizosphere microbial communities. a The experimental operation diagram of soil microbiota selection by plants; rhizosphere microbial richness: ACE index and number of species per sample (b); and relative abundance of the 10 most abundant microbial phyla (c) across three generations of Arabidopsis grown in microcosms. G-Wt-M represents microbiota in the corresponding generation of wild-type; G-pgr5-M represents microbiota in the corresponding generation of pgr5 Arabidopsis. Taxonomy details and significance analysis are shown in Additional file 2. Different letters represent significant differences (ANOVA followed by an LSD test; p < 0.05). Values are means ± SDs (n = 3)

Fig. 2

Verification of microbial function from the third generation. Number of days to the onset of flowering (i.e., when 80% of the control plants had floral buds of 1 cm or larger) (a, c) and shoot fresh weight (b, d) in wild-type (Wt) and two mutants (pnsB4 and pgr5) of Arabidopsis grown in microcosms in the presence of unsterilized soil slurry (WM and PM) (a, b) or sterilized soil slurry (WM-S and PM-S) (c, d) from the third generation. WM represents plants with microbiota isolates from wild-type plants in generation 3, PM represents the plants with microbiota isolates from pgr5 plants in generation 3, WM-S represents wild-type Arabidopsis grown with sterilized soil slurry, and PM-S represents Arabidopsis pgr5 mutants grown with sterilized soil slurry. Relative abundance of genes involved in N cycling (e amoA, ammonia oxidation; f nifH, N fixation; g nirK, nitrite reductase; h nosZ, nitrous oxide reductase) in soil samples of Wt and two mutant (pnsB4 and pgr5) lines of Arabidopsis grown in microcosms with the addition of unsterilized rhizosphere soil slurries of wild-type (WM) and mutant (PM) Arabidopsis cultures. Asterisk represents a significant difference between WM and PM (p < 0.05). Values are means ± SDs (n = 9 with 20 Arabidopsis plants per sample)

Fig. 3

N availability could be influenced by the addition of microbiota from the third generation. NH₄⁺-N content (A), urease activity (B), NO₃⁻-N content (C), and nitrate reductase activity (D) after inoculation for the WM- and PM-treated groups in the three Arabidopsis lines (Wt, pnsB4, and pgr5) (n = 12). Different letters represent significant differences (p < 0.05). The red symbols represent the WM-treated samples, and the blue symbols represent the PM-treated samples

Fig. 4

Root exudates of the two Arabidopsis lines. a Principal component analysis (PCA) of root exudates in the Wt and pgr5 treatments (n = 6) grown hydroponically. b Differentially released exudates (p < 0.05) in the Wt and pgr5 treatments were classified into corresponding metabolic pathways inferred from the KEGG pathway database (n = 6). c Tryptophan (Trp) and indole-3-acetic acid (IAA) contents in the soil of the cultures of Wt Arabidopsis or pgr5 mutants grown for three generations in microcosms. d Trp and IAA contents in the soil-cultured Wt Arabidopsis for one generation that had been in advance added the microbiota from the Wt (WM) or the pgr5 mutant (PM) Arabidopsis. Red and blue bars indicate that the exudates for a given pathway are mainly up- or downregulated, respectively, in the Wt cultures relative to the pgr5 mutant cultures. The blue and red vertical dashed lines depict p = 0.05 (−log (0.05) = 1.3) and p = 0.01 (−log (0.01) = 2), respectively. Asterisk represents a significant difference (p < 0.05). Values are means ± SDs (n = 6)

Fig. 5

IAA delayed flowering time by downregulating genes involved in flowering. a Proportion of bolting (i.e., percentage of plants had floral buds of 1 cm or larger). Plants were hydroponically grown in MS medium containing 5 nM and 25 nM IAA. b Relative rates of transcription of genes involved in flowering in Wt Arabidopsis at the early, intermediate (Int.), and late stages of flowering after one generation of culture. Plants were hydroponically grown in MS medium containing 5 nM IAA. All transcription levels are normalized to that of a housekeeping gene (actin 2). Values are means ± SDs (n = 6). Asterisk represents a significant difference (p < 0.05)

Fig. 6

Schematics of interactions between plants and rhizosphere microbiota. The proposed community/function relationships for rhizosphere microorganisms and their interaction with plant physiology and floral phenology through root exudates, N cycling, and production of the phytohormone IAA