Cristina Andrés-Barrao, Hanin Alzubaidy, Rewaa Jalal, Kiruthiga G. Mariappan, Axel de Zélicourt, Ameerah Bokhari, Olga Artyukh, Khairiah Alwutayd, Anamika Rawat, Kirti Shekhawat, Marília Almeida-Trapp, Maged M. Saad, and Heribert Hirt

PNAS November 16, 2021 118 (46) e2107417118

Significance

Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant.

Abstract

Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.

See: https://www.pnas.org/content/118/46/e2107417118

Fig. 1.

Scheme of experimental setup: SA187 was incubated in 1/2MS without (B) or with 100 mM NaCl (SB) for 4 h at 28 °C. Arabidopsis seedlings were germinated for 5 d, with or without SA187 before transfer to fresh 1/2MS plates for 12 d without (P, PB) or with 100 mM NaCl (SP, SPB) and vertically grown for 12 d (22 °C, 16/8 h light/dark cycle) (A). Volcano plots of SA187 DEGs in free-living and endophytic conditions with and without salt: to analyze the effect of salinity, SA187 in 1/2MS + 100 mM NaCl (salt stress) was compared to SA187 grown in 1/2MS (mock) in both free-living and plant-associated conditions (B). MA plots: representation of the gene expression fold change (M-axis) versus the mean gene expression values (A-axis) for each comparison. Dotted blue line marks the differential expression fold change = 2 [log2(fold change) = 1], those genes showing M > 1 as up-regulated and M < −1 as down-regulated. M = log2(log10(FPKM2)/(log10(FPKM1)), A = 1/2log2(log10(FPKM1)*log10(FPKM2)). Zero values of FPKM were ignored. Scatter plots were generated with R (Rstudio version 1.0.136) (C). Venn diagram showing up- and down-regulated genes that are common or specific for mock and salt stress conditions, comparing SA187 endophytic to free-living state (q-value <0.05) (D). KO functional analysis: metabolic processes regulated in response to the adaptation to the plant-associated lifestyle under nonsalt (PB versus B) and salt stress conditions (SPB versus SB) (E). Metabolic processes up- and down-regulated in response to plant associations that are common in both control and salt stress conditions (Left) or specific to control condition (Center) or salt stress (Right) (F). y-axis = KEGG functional categories. x-axis = number of genes or KO identifiers in KEGG knowledgebase from each subset of regulated genes in our analysis. Up-regulated metabolic processes are in red and down-regulated in blue.