Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes / -bacteria (PGPR), resulting in priming of defense or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze hundreds of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events.

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The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance.

The review analyses data on physiological and biochemical influence of rhizospheric and endophytic plant growth promoting rhizobacteria (PGPR) on induced the mechanisms of resistance of plants and the possibility of their using in agricultural for to protect crop from pathogens and phytophages. Resistance of plants promoted by PGPR due to their endosymbiotic interrelationships is directly achieved by producing peptide antibiotics and hydrolases of chitin and glucan and also because plants form their own system of induced resistance, accompanied by changes in the balance of defensive proteins, phytohormones, and pro-/antioxidant status.

Plant growth promoting rhizobacteria as alternative to chemical crop protectors from pathogens (review)

Bacillus velezensis is an aerobic, gram-positive, endospore-forming bacterium that promotes plant growth. Numerous strains of this species have been reported to suppress the growth of microbial pathogens, including bacteria, fungi, and nematodes. Based on recent phylogenetic analysis, several Bacillus species have been reclassified as B. velezensis. However, this information has yet to be integrated into a well-organized resource. Genomic analysis has revealed that B. velezensis possesses strain-specific clusters of genes related to the biosynthesis of secondary metabolites, which play significant roles in both pathogen suppression and plant growth promotion. More specifically, B. velezensis exhibits a high genetic capacity for synthesizing cyclic lipopeptides (i.e., surfactin, bacillomycin-D, fengycin, and bacillibactin) and polyketides (i.e., macrolactin, bacillaene, and difficidin). Secondary metabolites produced by B. velezensis can also trigger induced systemic resistance in plants, a process by which plants defend themselves against recurrent attacks by virulent microorganisms. This is the first study to integrate previously published information about the Bacillus species, newly reclassified as B. velezensis, and their beneficial metabolites (i.e., siderophore, bacteriocins, and volatile organic compounds).

Bacillus velezensis: A valuable member of bioactive molecules within plant microbiomes

Eleven bacterial strains were isolated at different soil depths from roots and rhizosphere of grapevines from a commercial vineyard. By 16S rRNA gene sequencing 10 different genera and 8 possible at species level were identified. From them, Bacillus licheniformis Rt4M10 and Pseudomonas fluorescens Rt6M10 were selected according to their characteristics as plant growth promoting rhizobacteria (PGPR). Both produced abscisic acid (ABA), indole-3-acetic acid (IAA) and the gibberellins A1 and A3 in chemically-defined medium. They also colonized roots of in vitro grown Vitis vinifera cv. Malbec plants. As result of bacterization ABA levels in 45 days-old in vitro plants were increased 76-fold by B. licheniformis and 40-fold by P. fluorescens as compared to controls. Both bacteria diminished plant water loss rate in correlation with increments of ABA. Twenty and 30 days post bacterization the plants incremented terpenes. The monoterpenes α-pinene, terpinolene, 4-carene, limonene, eucalyptol and lilac aldehyde A, and the sesquiterpenes α-bergamotene, α-farnesene, nerolidol and farnesol were assessed by gas chromatography-electron impact mass spectrometry analysis. α-Pinene and nerolidol were the most abundant (µg per g of tissue in plants bacterized with P. fluorescens). Only α-pinene, eucalyptol and farnesol were identified at low concentration in non-bacterized plants treated with ABA, while no terpenes were detected in controls. The results obtained along with others from literature suggest that B. licheniformis and P. fluorescens act as stress alleviators by inducing ABA synthesis so diminishing water losses. These bacteria also elicit synthesis of compounds of plant defense via an ABA independent mechanism.

Bacteria isolated from roots and rhizosphere of Vitis vinifera retard water losses, induce abscisic acid accumulation and synthesis of defense-related terpenes in in vitro cultured grapevine.

Several endophytic bacteria reportedly induce resistance to biotic stress and abiotic stress tolerance in several plant species. Burkholderia phytofirmans PsJN is a plant-growth-promoting rhizobacterium (PGPR) that is able to colonize grapevine tissues and induce resistance to gray mold. Further, PsJN induces physiological changes that increase grapevine tolerance to low nonfreezing temperatures. To better understand how bacteria induced the observed phenomena, stress-related gene expression and metabolite accumulation were monitored in 6-week-old Chardonnay grapevine plantlets after exposure to low nonfreezing temperatures. Under normal conditions (26°C), plantlet bacterization had no significant effect on the monitored parameters. By contrast, at 4°C, both stress-related gene transcripts and metabolite levels increased earlier and faster, and reached higher levels in PsJN-bacterized plantlets than in nonbacterized counterparts, in accordance with priming phenomena. The recorded changes may be correlated with the tolerance to cold stress conferred by the presence of PsJN. This is the first time that PGPR-induced priming has been shown to protect plants against low-temperature stress. Moreover, 1 week after cold exposure, levels of stress-related metabolites had declined more in PsJN-bacterized plants, suggesting that the endophyte is involved in the cold acclimation process via the scavenging system.

https://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-11-0124

Burkholderia phytofirmans PsJN Primes Vitis vinifera L. and Confers a Better Tolerance to Low Nonfreezing Temperatures

Non-pathogenic rhizobacteria Pseudomonas spp. can reduce disease in plant tissues through induction of a defence state known as induced systemic resistance (ISR). This resistance is based on multiple bacterial determinants, but nothing is known about the mechanisms underlying rhizobacteria-induced resistance in grapevine. In this study, the ability of Pseudomonas fluorescens CHA0 and Pseudomonas aeruginosa 7NSK2 to induce resistance in grapevine against Botrytis cinerea is demonstrated. Both strains also triggered an oxidative burst and phytoalexin (i.e. resveratrol and viniferin) accumulation in grape cells and primed leaves for accelerated phytoalexin production upon challenge with B. cinerea. Treatment of cell cultures with crude cell extracts of bacteria strongly enhanced oxidative burst, but resulted in comparable amounts of phytoalexins and resistance to B. cinerea to those induced by living bacteria. This suggests the production of bacterial compounds serving as inducers of disease resistance. Using other strains with different characteristics, it is shown that P. fluorescens WCS417 (Pch-deficient), P. putida WCS358 (Pch- and SA-deficient) and P. fluorescens Q2-87 (a DAPG producer) were all capable of inducing resistance to an extent similar to that induced by CHA0. However, in response to WCS417 (Pch-negative) the amount of H2O2 induced is less than for the CHA0. WCS417 induced low phytoalexin levels in cells and lost the capacity to prime for phytoalexins in the leaves. This suggests that, depending on the strain, SA, pyochelin, and DAPG are potentially effective in inducing or priming defence responses. The 7NSK2 mutants, KMPCH (Pch- and Pvd-negative) and KMPCH-567 (Pch-, Pvd-, and SA-negative) induced only partial resistance to B. cinerea. However, the amount of H2O2 triggered by KMPCH and KMPCH-567 was similar to that induced by 7NSK2. Both mutants also led to a low level of phytoalexins in grapevine cells, while KMPCH slightly primed grapevine leaves for enhanced phytoalexins. This highlights the importance of SA, pyochelin, and/or pyoverdin in priming phytoalexin responses and induced grapevine resistance by 7NSK2 against B. cinerea.

Pseudomonas spp.-induced systemic resistance to Botrytis cinerea is associated with induction and priming of defence responses in grapevine

Verhagen, B., Trotel-Aziz, P., Jeandet, P., Baillieul, F., and Aziz, A. 2011. Improved resistance against Botrytis cinerea by grapevine-associated bacteria that induce a prime oxidative burst and phytoalexin production. Phytopathology 101:768-777. Bacteria such as Pantoea agglomerans (Pa-AF2), Bacillus subtilis (Bs271), Acinetobacter lwoffii (Al-113), and Pseudomonas fluorescens (PfCT2), originating from the vineyard, can induce defense responses and enhance resistance of grapevine against the fungal pathogen Botrytis cinerea. The perception of these bacteria by plant cells or tissues in relation to their activities remains unknown. In this study, we examined the relationships between the activity of each bacterium to induce or prime some defense responses, and its effectiveness to induce resistance in grapevine against B. cinerea. We showed that all selected bacteria are capable of inducing early oxidative burst and phytoalexin (transresveratrol and trans-e-viniferin) production in grapevine cells and leaves. Pf-CT2 and Al-113 induced higher H2O2 and trans-resveratrol accumulations, and were able to further prime plants for accelerated phytoalexin production after B. cinerea challenge. These two bacteria were also the most effective in inducing local and systemic resistance. A similar level of induced resistance was observed with live Pa-AF2 which also induced but not primed a greater accumulation of trans-resveratrol. However, Bs-271, which was less effective in inducing resistance, induced a lower trans-resveratrol synthesis, without priming activity. Treatment of grapevine cells with growing medium or crude extract of the bacteria quickly and strongly enhanced oxidative burst compared with the live bacteria. However, both treatments resulted in comparable amounts of phytoalexins and induced local and systemic resistance to B. cinerea as compared with those induced by living bacteria, with extracts from PfCT2 and Al-113 being the most effective. Together, these results indicate that induced resistance can be improved by treatment with bacteria or derived compounds which induced or primed plants for enhanced phytoalexin accumulation.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-09-10-0242

Improved Resistance Against Botrytis cinerea by Grapevine-Associated Bacteria that Induce a Prime Oxidative Burst and Phytoalexin Production

The rhizospheric Bacillus subtilis PTA-271 (271) and endophytic Pseudomonas fluorescens PTA-CT2 (CT2) and Pantoea agglomerans PTA-AF2 (AF2) bacteria are able to induce systemic resistance (ISR) in grapevine against B. cinerea, but ISR markers and their costs remained unknown in vineyards. In this study, we investigated the relationship between the effectiveness of single and binary combinations of selected bacteria to induce ISR and their ability to trigger phytoalexin accumulation, as a potential marker for disease resistance, in leaves and berries, as well as their impact on grape yield in vineyards.
 Grapevine plants were treated during 2006 in two vineyards by drenching soil with single or binary mixtures of bacteria. Induced resistance against B. cinerea was evaluated and stilbenic phytoalexins were analyzed by HPLC in both leaves and berries. Grape yield was also assessed as number and weight of clusters at ripening. Both single and mixtures of bacteria were effective in reducing gray mold severity in the leaves and berries in vineyards. Disease control was accompanied by a significant accumulation of stilbenic phytoalexins, trans-resveratrol and e-viniferin, in both leaves and berries in the bacterized plants. δ-Viniferin also accumulated, but only in berries of the treated plants. Reduction of disease symptoms and accumulation of resveratrol and viniferins were higher in the plants treated with single CT2 compared to AF2 and 271. Treatment of grapevine plants with binary mixtures of these isolates resulted in a significant performance of CT2+AF2 in leaves and CT2+271 in berries. On the other hand, bacterial treatments did not show any negative effect on grape yield. These results revealed the efficacy of CT2 alone or in combination with AF2 or with 271 in triggering grapevine resistance against B. cinerea and enhancing systemic accumulation of resveratrol and viniferins, without compromising grape yield.

Effectiveness of beneficial bacteria to promote systemic resistance of grapevine to gray mold as related to phytoalexin production in vineyards

[Abstract] Grapevine (Vitis vinifera L.) is susceptible to an array of diseases among them the grey mold caused by the necrotrophic fungus Botrytis cinerea that decreases grape productivity and quality. To ensure a satisfactory yield and harvest quality numerous chemical fungicides are required, but they have serious drawbacks. One alternative is the use of beneficial bacteria to improve plant health. Pseudomonas fluorescens has been shown to trigger a plant-mediated resistance response in aboveground plant tissues against fungal, oomycete, bacterial, and viral pathogens. Triggered plant resistance exploits mechanisms of the plant immune system through a priming state that provides plants with enhanced capacity for rapid and strong activation of defense responses after pathogen infection, resulting in a lower fitness-cost. The primed responses by beneficial bacteria include induced expression of defense-related genes, cell wall reinforcement, and the production of secondary metabolites after pathogen infection. In this protocol, we describe the experimental design to evaluate the priming state of grapevine plants by the beneficial bacterium Pseudomonas fluorescens PTA-CT2 and their resistance level to Botrytis cinerea according to Verhagen et al. (2011) and Gruau et al. (2015).

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Bas Verhagen

Papers

Pseudomonas spp.-induced systemic resistance to Botrytis cinerea is associated with induction and priming of defence responses in grapevine

Improved Resistance Against Botrytis cinerea by Grapevine-Associated Bacteria that Induce a Prime Oxidative Burst and Phytoalexin Production

Effectiveness of beneficial bacteria to promote systemic resistance of grapevine to gray mold as related to phytoalexin production in vineyards

An Assay to Study Botrytis cinerea-infected Grapevine Leaves Primed with Pseudomonas fluorescens