Publications of Marc Ongena
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See detailUnravelling chemical mechanisms in microbial interactions by combining thin layer chromatography, ion mobility and MALDI imaging mass spectrometry
Mc Cann, Andréa ULiege; Kune, Christopher ULiege; La Rocca, Raphaël ULiege et al

Conference (2020, June 01)

Mass spectrometry (MS) is a method of choice in microbiology for untargeted detection and identification of bioactive compounds. Mass Spectrometry Imaging (MSI) has led to a growing interest in the in ... [more ▼]

Mass spectrometry (MS) is a method of choice in microbiology for untargeted detection and identification of bioactive compounds. Mass Spectrometry Imaging (MSI) has led to a growing interest in the in situ study of biomolecules produced when microorganisms interact with each other. However, in situ identification is still time-consuming and challenging due to the large chemical diversity contained in each pixel of the samples, resulting in very complex average MS spectra. Here, we propose to exploit the power of combining Kendrick Mass Defect (KMD) analysis and collision cross section (CCS) values using mobility for the characterization of families of related compounds in MSI. The identification of compounds was supported by rapid thin layer chromatography (TLC) separation coupled to MALDI-MS/MS detection. Bacillus velezensis GA1 and Pseudomonas sp. CMR12a were inoculated at different distances (0.5, 1 and 2 cm) on a semi-solid agar-based medium and incubated at 30°C. Regions of interest were cut directly from the Petri dish and transferred to the target ITO plate. This assembly was placed in a vacuum desiccator until completely dry and covered with HCCA matrix (Sunchrom sprayer). Ion mobility in imaging mode was performed using the timsTOF fleX (Bruker Daltonics, Bremen, Germany). TLC separation of ROI extracts is analyzed by MALDI-MS/MS imaging on the rapifleX instrument (Bruker Daltonics) for rapid screening of compounds and on the solariX instrument (Bruker Daltonics) for exact mass and isotopic distribution. The data were processed and integrated with in-house software. The coupling of MALDI-MSI with ion mobility separation brings additional structural features/information. It allows data to be filtered according to a range of CCS values and it improves the confidence level for the identification of detected analytes, in addition to exact mass determination. A relationship between CCS and mass was also performed. In combination with KMD analysis, various families of compounds, such as lipids or lipopeptides could be automatically detected and identified. Through this workflow, the comparison of the three different culture conditions was greatly simplified and highlighted the changes that occur in the metabolism of the bacteria. In particular, we were able to observe a variation within the lipid composition of Pseudomonas sp. CMR12a as a function of distance from the Bacillus velezensis GA1 colony. Finally, TLC separation was successfully optimized for lipopeptides and lipids and validated the identification of detected compounds by simplifying the spectra and allowing image analysis. TLC also enables high throughput, in part due to the parallel imaging of up to 6 traces on a single TLC run. TLC plate matrix coating strategies were compared to optimize the MALDI MS signal. This workflow will also be applied to time-lapse (or time-dependent) experiments, to monitor the bioactive compounds production and migration as a function of the co-culture interaction time. [less ▲]

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See detailInduced Systemic Resistance by a Plant Growth-Promoting Rhizobacterium Impacts Development and Feeding Behavior of Aphids
Serteyn, Laurent ULiege; Quaghebeur, Céleste; Ongena, Marc ULiege et al

in Insects (2020), 11(4),

The effects of microorganisms on plant-insect interactions have usually been underestimated. While plant growth-promoting rhizobacteria (PGPR) are known to induce plant defenses, endosymbiotic bacteria ... [more ▼]

The effects of microorganisms on plant-insect interactions have usually been underestimated. While plant growth-promoting rhizobacteria (PGPR) are known to induce plant defenses, endosymbiotic bacteria hosted by herbivorous insects are often beneficial to the host. Here, we aimed to assess whether PGPR-induced defenses in broad bean plants impact the pea aphid, depending on its genotype and the presence of endosymbionts. We estimated aphid reproduction, quantified defense- and growth-related phytohormones by GC-MS, and measured different plant growth and physiology parameters, after PGPR treatment. In addition, we recorded the feeding behavior of aphids by electropenetrography. We found that the PGPR treatment of broad bean plants reduced the reproduction of one of the pea aphid clones. We highlighted a phenomenon of PGPR-induced plant defense priming, but no noticeable plant growth promotion. The main changes in aphid probing behavior were related to salivation events into phloem sieve elements. We suggest that the endosymbiont Hamiltonella defensa played a key role in plant-insect interactions, possibly helping aphids to counteract plant-induced resistance and allowing them to develop normally on PGPR-treated plants. Our results imply that plant- and aphid-associated microorganisms add greater complexity to the outcomes of aphid-plant interactions. [less ▲]

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See detailLinolenic fatty acid hydroperoxide acts as biocide on plant pathogenic bacteria: biophysical investigation of the mode of action
Deboever, Estelle ULiege; Lins, Laurence ULiege; Ongena, Marc ULiege et al

in Bioorganic Chemistry (2020)

Fatty acid hydroperoxides (HPO) are free phyto-oxylipins known for their crucial role as signalling molecules during plant defense mechanisms. They were also demonstrated to have direct biocidal ... [more ▼]

Fatty acid hydroperoxides (HPO) are free phyto-oxylipins known for their crucial role as signalling molecules during plant defense mechanisms. They were also demonstrated to have direct biocidal activities against plant pathogens including gram negative bacteria. In the present work, the biocidal effect of one linolenic fatty acid hydroperoxide, namely 13-HPOT has been investigated on three plant pathogen gram negative bacteria: Pectobacterium carotovorum, Pseudomonas syringae and Xanthomonas translucens. We showed that 13-HPOT has a strong dose response effect on those phytopathogens. In a second part, the molecular mechanism behind the antibacterial effect of 13-HPOT was investigated at a molecular level using an integrative biophysical approach combining in vitro and in silico methods. Since other antimicrobial amphiphilic molecules have been shown to target the lipid membrane of the organisms they act on, we focused our study on the interaction of 13-HPOT with biomimetic membranes. In a first step, we hypothesized that the inner membrane of the bacteria was the main site of action of 13-HPOT and hence we used lipids representative of this membrane to form our models. Our results indicated that 13-HPOT can interact with the lipid representative of the inner bacterial plasma membrane. A strong membrane insertion is suggested but no major permeabilization of the membrane is observed. Phosphatidylethanolamine (PE) and cardiolipin (CL), present in the bacterial plasma membrane, appear to play important roles in this interaction. We suggest that the mode of action of 13-HPOT should involve either subtle changes in membrane properties, such as its lateral organization and distribution, and/or interactions with membrane proteins. [less ▲]

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See detailRapid identification of chemically-related compounds produced by bacteria by Kendrick mass defect filtering applied to high resolution imaging mass spectrometry
Mc Cann, Andréa ULiege; Kune, Christopher ULiege; La Rocca, Raphaël ULiege et al

Poster (2019, October 30)

Introduction Over the last years, lots of progress have been done in the development of mass spectrometry imaging, making the technique more and more accessible for various applications, such as ... [more ▼]

Introduction Over the last years, lots of progress have been done in the development of mass spectrometry imaging, making the technique more and more accessible for various applications, such as biomarkers discovery or bioactive compounds identification. However, the progresses made in terms of spatial and instrumental resolution has for consequences the dramatic increase of dataset size, shifting the burden from data production to data analysis and compounds identification. We propose here to use a semi-targeted method based on Kendrick mass defect (KMD) analysis to immediately identify the chemistry-related compounds in mass spectrometry imaging applied to microbiology samples. Thanks to a software developed in-house, we are now able to better understand the bacteria-bacteria interactions. Materials and methods Bacteria strains were inoculated on a semi-solid agar-based medium and incubated at 30°C. Region of interest was cut directly from the petri dish and transferred to the target ITO plate, previously covered with double sided conductive carbon tape. This assembly was then put in a vacuum desiccator until complete drying (overnight), and covered with HCCA matrix. Mass spectrometry images were obtained using a FT-ICR mass spectrometer (9.4T SolariX, Bruker Daltonics, Bremen, Germany). Data analysis was performed on an in-house software. Results & Discussion KMD filtering for mass spectrometry imaging enabled the rapid identification of chemically-related compounds such as lipopeptides or lipids, independently of the signal intensity and without the need of an extensive database search. For each detected family of compounds, an image was generated, enabling to link the chemically-related compounds identified with their spatial localization. The analysis of the bacteria-bacteria interaction was greatly simplified by our in-house software, and we were able to have a better understanding of the underlying chemical mechanisms involved. [less ▲]

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See detailRapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect As a Filter in Mass Spectrometry Imaging
Kune, Christopher ULiege; Mc Cann, Andréa ULiege; La Rocca, Raphaël ULiege et al

in Analytical Chemistry (2019), 91(20), 13112-13118

Kendrick mass defect (KMD) analysis is widely used for helping the detection and identification of chemically related compounds based on exact mass measurements. We report here the use of KMD as a ... [more ▼]

Kendrick mass defect (KMD) analysis is widely used for helping the detection and identification of chemically related compounds based on exact mass measurements. We report here the use of KMD as a criterion for filtering complex mass spectrometry data set. The method allow automated, easy and efficient data processing, enabling the reconstruction of 2D distributions of families of homologous compounds from MSI images. We show that KMD filtering, based on in-house software, is suitable and robust for high resolution (full width at half-maximum, fwhm, at m/z 410 of 20 000) and very high-resolution (fwhm, at m/z 410 of 160 000) MSI data. This method has been successfully applied to two different types of samples, bacteria cocultures, and brain tissue sections. [less ▲]

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See detailAstin C production by the endophytic fungus Cyanodermella asteris in planktonic and immobilized culture conditions
Vassaux, Antoine ULiege; Tarayre, Cédric; Arguelles Arias, Anthony ULiege et al

in Biotechnology Journal (2019)

The fungal endophyte Cyanodermella asteris was recently isolated from the medicinal plant Aster tataricus. This fungus produces astin C, a cyclic pentapeptide with anticancer and anti-inflammatory ... [more ▼]

The fungal endophyte Cyanodermella asteris was recently isolated from the medicinal plant Aster tataricus. This fungus produces astin C, a cyclic pentapeptide with anticancer and anti-inflammatory properties. The production of this secondary metabolite was compared in immobilized and planktonic conditions. For immobilized cultures, a stainless steel packing immersed in the culture broth was used as a support. In these conditions, the fungus exclusively grew on the packing, which provides a considerable advantage for astin C recovery and purification. C. asteris metabolism was different according to the culture conditions in terms of substrate consumption rate, cell-growth, and astin C production. Immobilized-cell cultures yielded a 30% increase of astin C production associate to a 39% increase in biomass. The inoculum type as spores rather than hyphae, and a pre-inoculation washing procedure with sodium hydroxide, turned out to be beneficial both for astin C production and fungus development onto the support. Finally, influence of culture parameters such as pH and medium composition, on astin C production was evaluated. With optimized culture conditions, astin C yield was further improved reaching a five times higher final specific yield compared to the value reported with astin C extraction from Aster tataricus (0.89 and 0.16 mg/g respectively). [less ▲]

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See detailComputational chemistry and ion mobility – mass spectrometry at high resolving power suggest prototropism of cyclic lipopeptides
Mc Cann, Andréa ULiege; Kune, Christopher ULiege; Far, Johann ULiege et al

Poster (2019, June)

Introduction Cyclic lipopeptides (CLPs) are cyclic hydrophilic peptides with a lipid ramification using a β-hydroxy fatty acid that are produced by bacteria in a ribosome independent manner. Despite CLPs ... [more ▼]

Introduction Cyclic lipopeptides (CLPs) are cyclic hydrophilic peptides with a lipid ramification using a β-hydroxy fatty acid that are produced by bacteria in a ribosome independent manner. Despite CLPs have relatively low molecular weight between 800 and 2,000 Da, the analysis of lipopeptides remains challenging due to the wide variety of synthetized isoforms differing in fatty acid chain length, in methyl group branching position, and in the nature of the amino-acids residues. These isoforms are suspected to have different biological activities requiring development of reliable methods for CLPs characterization. We present here an original approach combining UPLC and ion mobility - mass spectrometry at high resolving powers to separate the different species. Experimentally determined CCS will be compared with theoretical ones. Methods Lipopeptides were separated by UPLC (I-class, Waters, U.K.) on a C18 BEH column and identified by CID MS/MS mass spectrometry. Ion mobility – mass spectrometry (IM-MS) measurements were performed on a traveling wave ion mobility mass spectrometer (Synapt G2 HDMS from Waters, U.K.) and on a trapped Ion Mobility Mass Spectrometer (timsTOF, Bruker Daltonics, U.S.A.) to investigate the 3D structures of the ionized lipopeptides. Accurate Collison Cross Section (CCS) were obtained in both positive and negative mode and compared with theoretical CCS. Density Functional Theory (Gaussian) was used for structure optimizations at the CAM-B3LYP level of theory and 3-21G as basis set. Theoretical CCS have been computed from optimized structures using the trajectory method from IMoS V2. Preliminary data Separation of lipopeptides such as surfactins was successfully performed by reverse phase liquid chromatography. Lipopeptides were separated according to lipidic chain length and the branching position of the methyl group (iso/anteiso/linear). In positive ionization mode, the infusion of each isolated isoforms in the Synapt G2 showed a broad IMS distribution. These ion mobility profiles suggested the presence of different conformers. The higher IMS resolving power of the TIMS allowed the detection of at least three near-resolved peaks for a single isomer. In negative ionization mode however, only one peak was observed in the IM-MS profile on both Synapt G2 and TIMS, corresponding to one CCS. We included prototropic hypotheses where all the potential protonation and deprotonation sites on each lipopeptide had been determined by theoretical calculation. The abundances of the species in the CCS distributions of the resulting structures were obtained based on the Boltzmann distribution. Regarding the surfactin family, preliminary calculations by DFT shows that several protonation sites are energetically favorable and that the proton localization has a significant effect on the resulting CCS (∆CCS = 10Ų). These results are in good agreement with the experimental IMS profiles, obtained in both positive and negative ionization mode. Lipopeptides are then not related to a unique CCS value but a set of IM-MS profile that probably contains additional structural and physicochemical information. Novel aspect Experimental and theoretical approaches for lipopeptides IMS profiles analysis: protonation site determination, peaks intensity prediction and structural information extraction. [less ▲]

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See detailFrom noise to signal: Kendrick mass filtering for high-resolution mass spectrometry imaging analysis
Mc Cann, Andréa ULiege; Kune, Christopher ULiege; Arguelles Arias, Anthony ULiege et al

Poster (2019, April 14)

Introduction Over the last years, lots of progress have been done in the development of mass spectrometry imaging, making the technique more and more accessible for various applications, such as ... [more ▼]

Introduction Over the last years, lots of progress have been done in the development of mass spectrometry imaging, making the technique more and more accessible for various applications, such as biomarkers discovery or bioactive compounds identification. However, the progresses made in terms of spatial and instrumental resolution has for consequences the dramatic increase of dataset size, shifting the burden from data production to data analysis. We propose here to use a semi-targeted method based on Kendrick mass defect (KMD) analysis to immediately identify the chemistry-related compounds in mass spectrometry imaging applied to microbiology samples. Thanks to an in-house software, we are now able to better understand the bacteria-bacteria interactions. Materials and methods Bacillus velezensis GA1 and Pseudomonas sp. CMR12a were inoculated on a semi-solid agar-based medium and incubated at 30°C. Region of interest was cut directly from the petri dish and transferred to the target ITO plate, previously covered with double sided conductive carbon tape. This assembly was then put in a vacuum desiccator until complete drying (overnight), and covered with HCCA matrix. Mass spectrometry images were obtained using a FT-ICR mass spectrometer (9.4T SolariX, Bruker Daltonics, Bremen, Germany). Data analysis was performed on an in-house software. Results & Discussion Thanks to the KMD analysis, we were able to directly compare and identify the nature of the compounds detected in MSI such as lipids (1) or lipopeptides (2a), without the need of an extensive database search. It was also possible to identify some lipopeptides degradation occurring nearby Pseudomonas (2b). Thanks to our in-house software, the compounds with a similar chemistry can now be filtrated and the image can be reconstructed, removing thus the noise and focusing only on the signal. [less ▲]

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See detailLinoleic and linolenic acid hydroperoxides interact differentially with biomimetic plant membranes in a lipid specific manner
Deleu, Magali ULiege; Deboever, Estelle ULiege; Nasir, Mehmet Nail et al

in Colloids and Surfaces B: Biointerfaces (2019), 175

Linoleic and linolenic acid hydroperoxides (HPOs) constitute key intermediate oxylipins playing an important role as signaling molecules during plant defense processes in response to biotic or abiotic ... [more ▼]

Linoleic and linolenic acid hydroperoxides (HPOs) constitute key intermediate oxylipins playing an important role as signaling molecules during plant defense processes in response to biotic or abiotic stress. They have also been demonstrated in vitro as antimicrobial agents against plant fungi and bacteria. To reach the phytopathogens in vivo, the HPOs biosynthesized in the plant cells must cross the plant plasma membrane (PPM) where they can also interact with plasma membrane lipids and have an effect on their organization.In the present study, we have investigated the interaction properties of HPOs with PPM at a molecular level using biophysical tools combining in vitro and in silico approaches and using plant biomimetic lipid systems. Our results have shown that HPOs are able to interact with PPM lipids and perturb their lateral organization. Glucosylceramide (GluCer) is a privileged partner, sitosterol lessens their binding and the presence of both GluCer and sitosterol further reduces their interaction. Hydrophobic effect and polar interactions are involved in the binding. The chemical structure of HPOs influences their affinity for PPM lipids. The presence of three double bonds in the HPO molecule gives rise to a higher affinity comparatively to two double bonds, which can be explained by their differential interaction with the lipid polar headgroups. [less ▲]

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See detailSoil sterilization, pathogen and antagonist concentration affect biological control of Fusarium wilt of cape gooseberry by Bacillus velezensis Bs006
Moreno-Velandia, C. A.; Izquierdo-García, L. F.; Ongena, Marc ULiege et al

in Plant and Soil (2019)

Background and aim: Fusarium wilt (FW) is the major constraint on cape gooseberry (Physalis peruviana L.) production. Fungicides have been ineffective in disease control and alternative tools are not ... [more ▼]

Background and aim: Fusarium wilt (FW) is the major constraint on cape gooseberry (Physalis peruviana L.) production. Fungicides have been ineffective in disease control and alternative tools are not available. Bacillus velezensis (formerly Bacillus amyloliquefaciens) strain Bs006 has an antagonistic potential against Fusarium oxysporum f. sp. physali (Foph). However, results of in vivo tests have been variable. We examined the effect of biotic sources of variability on the biocontrol activity of Bs006. Methods: Pot experiments in greenhouse were carried out to determine the influence of soil sterilization and concentration of both pathogen and antagonist in soil on biocontrol activity and the effect of pathogen on plant growth promotion by Bs006. Results: Efficacy of Bs006 against FW was significantly lower under sterile than non-sterile soil condition. Diluted liquid culture of Bs006 at 1 × 106 and 1 × 107 cfu.mL−1 reduced FW by up to 97% under low Foph inoculum pressure (102 to 104 cfu.g−1 of soil) but at 1 × 108 cfu.mL−1 biological treatment significantly reduced FW only when the concentration of Foph was 1 × 104 cfu.g−1 by 71%. The evaluation of biomass of Bs006 (1 × 108 cfu.mL−1) and supernatant free of bacteria added at 10% allowed to observe that the supernatant was an additional source of biocontrol variability, since high volumes of supernatant favored the development of the disease. Plant growth promoting activity by Bs006 was reduced by the presence of Foph in the soil. Bs006 grew endophytically in cape gooseberry and had high population levels in the rhizosphere inoculated with Foph. Conclusions: The efficacy of Bs006 to reduce FW was affected by soil sterilization, the concentration of both antagonist and pathogen, and high volumes of supernatant. This work has practical implications for the design of control strategies based on B. velezensis Bs006. © 2018, The Author(s). [less ▲]

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See detailIdentification of Barley (Hordeum vulgare L. subsp. vulgare) Root Exudates Allelochemicals that are Actives against Weeds
Bouhaouel, Imen; Richard, Gaetan ULiege; Fauconnier, Marie-Laure ULiege et al

in Agronomy (2019), 9(7), 345-363

Crops with weed suppressive root exudates or the direct use of bioherbicidal allelochemicals is a new approach in integrated weed management systems. In this context, the allelopathic activity and ... [more ▼]

Crops with weed suppressive root exudates or the direct use of bioherbicidal allelochemicals is a new approach in integrated weed management systems. In this context, the allelopathic activity and chemical composition of root exudates from six genotypes (modern varieties and landraces) of barley were characterized. The phenolic acids appeared to be particularly implicated in the inhibitory action of barley root exudates against Bromus diandrus. The amount of these compounds was higher in sandy substrate than in sandy-clay-loam substrate. Ten phenolic acids and one phenylpropanoid derivative were present, in addition to saponarin, a newly identified flavonoid in barley root exudates. Seven compounds explaining variability in the inhibitory activity of barley roots (stepwise analysis) and one compound detected only in highly allelopathic genotypes were toxic against receiver plants. Most compounds had a greater inhibitory effect on the growth of great brome than the barley genotypes. The synergistic and/or additive effect of the eight compounds appeared to be the source of the toxicity. Benzoic acid, the mixture of compounds, saponarin and salicylic acid were the most effcient compounds against the great brome and the less aggressive against barley. Overall, the results revealed the allelopathic potential of the water-soluble compounds exuded by the roots of living barley plants. These compounds included saponarin, a flavonoid not yet recognized as a barley root allelochemical. [less ▲]

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See detailEffect of Plant Growth Promoting Rhizobacteria on aphids reproduction and feeding behaviour
Quaghebeur, Céleste; Serteyn, Laurent ULiege; Stouvenakers, Gilles ULiege et al

Poster (2018, August)

Some soil bacteria belonging to the Bacillus and Pseudomonas genera are particularly efficient biocontrol agents as Plant Growth Promoting Rhizobacteria (PGPR) by showing strong antagonistic activity ... [more ▼]

Some soil bacteria belonging to the Bacillus and Pseudomonas genera are particularly efficient biocontrol agents as Plant Growth Promoting Rhizobacteria (PGPR) by showing strong antagonistic activity toward plant pathogens and inducing systemic resistance (ISR). Beside plant pathogen microbial agents, phytophagous insects should also be impacted by ISR in host plants. Particularly, aphids are considered as herbivore models closed to fungal and bacterial plant pathogens when comparing host plant induced defense mechanisms after aphid attacks. Then, PGPR could play a primary role in interspecific interactions related to plants and aphids including changes in aphid behaviour. This poster shows the preliminary results of our work on interactions between PGPR, host plant and aphids. Among them, we can highlight the induction of phytohormones by PGPR application and the resulting changes in reproduction and feeding behavior of aphids. It seems that secundary endosymbionts play a preponderant role in aphid’s tolerance of elicitated plants. More researches are in progress, based on these trends. Further works will focus on the volatile organic compounds potentially involved in that response and their actual impact on host plant selection by aphids. [less ▲]

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See detailSynthetic Rhamnolipid Bolaforms trigger an innate immune response in Arabidopsis thaliana
Luzuriaga Loaiza, Walter ULiege; Schellenberger, Romain; De-Gaetano, Yannick et al

in Scientific Reports (2018), 8

Stimulation of plant innate immunity by natural and synthetic elicitors is a promising alternative to conventional pesticides for a more sustainable agriculture. Sugar-based bolaamphiphiles are known for ... [more ▼]

Stimulation of plant innate immunity by natural and synthetic elicitors is a promising alternative to conventional pesticides for a more sustainable agriculture. Sugar-based bolaamphiphiles are known for their biocompatibility, biodegradability and low toxicity. In this work, we show that Synthetic Rhamnolipid Bolaforms (SRBs) that have been synthesized by green chemistry trigger Arabidopsis innate immunity. Using structure-function analysis, we demonstrate that SRBs, depending on the acyl chain length, differentially activate early and late immunity-related plant defense responses and provide local increase in resistance to plant pathogenic bacteria. Our biophysical data suggest that SRBs can interact with plant biomimetic plasma membrane and open the possibility of a lipid driven process for plant-triggered immunity by SRBs. [less ▲]

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See detailIsolation and Identification of PGPR Strain and its Effect on Soybean Growth and Soil Bacterial Community Composition
Ma, Mingchao ULiege; Jiang, Xin; Wang, Qingfeng et al

in International Journal of Agriculture and Biology (2018), 20

Plant growth-promoting rhizobacteria (PGPR) are considered environmentally sound option to reduce chemical fertilizer inputs, improve soil quality and increase crop yields. The objective of this study was ... [more ▼]

Plant growth-promoting rhizobacteria (PGPR) are considered environmentally sound option to reduce chemical fertilizer inputs, improve soil quality and increase crop yields. The objective of this study was to isolate an effective PGPR strain and investigate its effects on soybean growth and soil bacterial community composition. A total of 163 bacterial isolates were obtained from rhizospheres of plants in four provinces of China. According to capacities for mineral potassium and phosphate solubilization, the best strain (designated 3016) was selected and identified as Paenibacillus mucilaginosus based on biochemical characterization and phylogenetic analysis. Moreover, strain 3016 showed a higher capacity for nitrogen fixation and phytohormone production than commercial strains. In a field experiment, P. mucilaginosus 3016 was used as an inoculant for seed dressing survived in the soybean rhizosphere as revealed by a species-specific PCR method. Inoculation significantly improved symbiotic nodulation, soybean growth parameters, nutrient contents and yields. The number of nodules was increased by 31.8% for the inoculation treatment compared with CK. Soybean height, pods and seeds per plant and dry weight of nodules were also significantly higher for the inoculation, as well as nutrient contents. Regarding yields, the highest of 3191.4 kg hm-2 was obtained under inoculation regime. Moreover, numerous bacterial classes and genera, which were associated with symbiotic nitrogen-fixation, plant growth promotion, biological control and soil catalase activity improvement, were also overrepresented in the inoculation treatment. Some taxa with negative impacts on soil quality decreased. In conclusion, inoculation with P. mucilaginosus 3016 had beneficial effects on both soybean growth and soil quality, and is a potential candidate for developing commercial inoculants of PGPR to be used as a bio-fertilizer. [less ▲]

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See detailEffect of long‑term fertilization strategies on bacterial community composition in a 35‑year field experiment of Chinese Mollisols
Ma, Mingchao ULiege; Zhou, jing; Ongena, Marc ULiege et al

in AMB Express (2018), 8(20),

Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is ... [more ▼]

Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM. [less ▲]

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See detailChronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols
Ma, Mingchao ULiege; Ongena, Marc ULiege; Wang, Qingfeng et al

in AMB Express (2018), 8(57),

Arbuscular mycorrhizal fungi (AMF) play vital roles in sustaining soil productivity and plant communities. However, adaption and differentiation of AMF in response to commonly used fertilization remain ... [more ▼]

Arbuscular mycorrhizal fungi (AMF) play vital roles in sustaining soil productivity and plant communities. However, adaption and differentiation of AMF in response to commonly used fertilization remain poorly understood. In this study, we showed that the AMF community composition was primarily driven by soil physiochemical changes associated with chronic inorganic and organic fertilization of 37 years in Mollisols. High-throughput sequencing indicated that inorganic fertilizer negatively affected AMF diversity and richness, implying a reduction of mutualism in plant–AMF symbiosis; however, a reverse trend was observed for the application of inorganic fertilizer combined with manure. With regards to AMF community composition, order Glomerales was dominant, but varied significantly among different fertilization treatments. All fertilization treatments decreased family Glomeraceae and genus Funneliformis, while Rhizophagus abundance increased. Plant-growth-promoting-microorganisms of family Claroideoglomeraceae and genus Claroideoglomus were stimulated by manure application, and likely benefited pathogen suppression and phosphorus (P) acquisition. Family Gigasporaceae and genus Gigaspora were negatively correlated with available P in soil. Additionally, redundancy analysis further suggested that soil available P, organic matter and pH were the most important factors in shaping AMF community composition. These results provide strong evidence for niche differentiation of phylogenetically distinct AMF populations under different fertilization regimes. Manure likely contributes to restoration and maintenance of plant–AMF symbiosis, and the balanced fertilization would favor the growth of beneficial AMF communities as one optimized management in support of sustainable agriculture in Mollisols. [less ▲]

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See detailResponses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols
Ma, Mingchao ULiege; Jiang, Xin; Wang, Qingfeng et al

in MicrobiologyOpen (2018), e597

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing ... [more ▼]

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal ommunity. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and (ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant–fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition. [less ▲]

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