Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, little is known about whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria. Here we show that flavonoids broadly contribute to the diversity of the Arabidopsis root microbiome and preferentially attract Aeromonadaceae, which included a cultivable Aeromonas sp. H1 that displayed flavonoid-induced chemotaxis with transcriptional enhancement of flagellum biogenesis and suppression of fumarate reduction for smooth swims. Strain H1 showed multiple plant-beneficial traits and enhanced plant dehydration resistance, which required flavonoids but not through a sudden “cry-for-help” upon stress. Strain H1 boosted dehydration-induced H2O2 accumulation in guard cells and stomatal closure, concomitant with synergistic induction of jasmonic acid-related regulators of plant dehydration resistance. These findings revealed a key role of flavonoids, and the underlying mechanism, in mediating plant-microbiome interactions including the bacteria-enhanced plant dehydration resistance.

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High levels of crop productivity cannot be sustained by chemical fertiliser application alone. In order to mitigate this, a 2-year study was conducted to test the effects of combined application of indigenous plant-growth-promoting rhizobacteria (PGPR) and chemical fertilisers on productivity of wheat and soil properties. Ten morphologically distinct indigenous PGPR isolates from wheat roots and rhizosphere were evaluated at Solan, Himachal Pradesh, India, during 2013–14. Three PGPR isolates (B2, SIR1 and BIS2) with maximum PGP traits were screened at different doses of nitrogen (N) and phosphorus (P) (80%, 60% and 40% of recommended fertiliser dose, RFD) under net-house conditions. Two isolates, B2 (Serratia sp.) and SIR1 (Bacillus subtilis), along with the optimum NP dose (i.e. 80% RFD) were selected for field experimentation, which was performed over two consecutive years, 2014–16. Combined application of 80% RDF of NP with PGPR (B2) significantly increased wheat yield by 9.4%, number of tillers per plant by 28.03%, grain number per spike by 19.61%, 1000-grain weight by 10.5%, and biomass by 9.2% relative to the uninoculated control with 100% RFD. Soil properties in the terms of available N, P and potassium, microbial biomass carbon, soil enzyme activities and population of phosphate-solubilising bacteria in the wheat crop were significantly increased by the combined application of bacterial inoculants with 80% RFD of NP in both years over the uninoculated control. Therefore, the results revealed the potential of indigenous PGPR isolates to supplement ~20% of NP fertilisers without hampering the soil fertility and productivity of wheat.

A study was executed in a direction to attenuate Sclerotinia stalk rot (SSR) disease through biocontrol agent and also to enhance crop productivity. Culture filtrate of bacterial strain YSPMK11 inhibited growth of Sclerotinia sclerotiorum in vitro which also exhibited higher plant growth promoting attributes. Interaction studies revealed maximum (81.50%) growth inhibition at 35°C and pH 7.0 after 72 h incubation period with 15% culture filtrate. Based upon 16S rRNA gene sequence strain, YSPMK11 was identified as Bacillus pumilus. Furthermore, the genome of this isolate was searched for antimicrobial lipopeptide, i.e., ItuD and SrfC genes. The PCR amplification results showed the presence of both these lipopeptide genes in isolate YSPMK11. Iturin A as antifungal compound was identified as major components of fraction through GC/MS. In field experiments, the application of strain YSPMK11 cell suspension (10 8 CFU/ml) suppressed disease severity by 93% and increased curd yield by 36% which was more that of commercially used fungicide in farmer practices under mid-hills of Himachal Pradesh.Conclusively, our study is first to demonstrate the effect of B. pumilus strain YSPMK11 in suppression of SSR under field conditions and would be employed as an efficient biocontrol agent to replace commercial fungicides in cauliflower cropping system. In addition, the presence of both lipopeptide genes (ItuD and SrfC) and iturin A in this isolate makes him potent strain for biological control application in agriculture.

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Background Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors regulate the readouts of genetic information and consequently many essential biological processes. However, it has been elusive whether RNA-directed DNA methylation (RdDM) affects root microbiota assembly. Results By applying 16S rRNA gene sequencing, we investigated root microbiota of Arabidopsis mutants defective in the canonical RdDM pathway, including dcl234 that harbors triple mutation in the Dicer-like proteins DCL3, DCL2, and DCL4, which produce small RNAs for RdDM. Alpha diversity analysis showed reductions in microbe richness from the soil to roots, reflecting the selectivity of plants on root-associated bacteria. The dcl234 triple mutation significantly decreases the levels of Aeromonadaceae and Pseudomonadaceae, while it increases the abundance of many other bacteria families in the root microbiota. However, mutants of the other examined key players in the canonical RdDM pathway showed similar microbiota as Col-0, indicating that the DCL proteins affect root microbiota in an RdDM-independent manner. Subsequently gene analysis by shotgun sequencing of root microbiome indicated a selective pressure on microbial resistance to plant defense in the dcl234 mutant. Consistent with the altered plant-microbe interactions, dcl234 displayed altered characters, including the mRNA and sRNA transcriptomes that jointly highlighted altered cell wall organization and up-regulated defense, the decreased cellulose and callose deposition in root xylem, and the restructured profile of root exudates that supported the alterations in gene expression and cell wall modifications. Conclusion Our findings demonstrate an important role of the DCL proteins in influencing root microbiota through integrated regulation of plant defense, cell wall compositions, and root exudates. Our results also demonstrate that the canonical RdDM is dispensable for Arabidopsis root microbiota. These findings not only establish a connection between root microbiota and plant epigenetic factors but also highlight the complexity of plant regulation of root microbiota.

Water deficit is one of the major constraints to crop production and food security worldwide. Some plant growth-promoting rhizobacteria (PGPR) strains are capable of increasing plant drought resistance. Knowledge about the mechanisms underlying bacteria-induced plant drought resistance is important for PGPR applications in agriculture. In this study, we show the drought stress-mitigating effects on tomato plants by the Bacillus megaterium strain TG1-E1, followed by the profiling of plant transcriptomic responses to TG1-E1 and the profiling of bacterial extracellular metabolites. Comparison between the transcriptomes of drought-stressed plants with and without TG1-E1 inoculation revealed bacteria-induced transcriptome reprograming, with highlights on differentially expressed genes belonging to the functional categories including transcription factors, signal transduction, and cell wall biogenesis and organization. Mass spectrometry-based analysis identified over 40 bacterial extracellular metabolites, including several important regulators or osmoprotectant precursors for increasing plant drought resistance. These results demonstrate the importance of plant transcriptional regulation and bacterial metabolites in PGPR-induced plant drought resistance.