A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium.
ABSTRACT: Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.
Project description:The successful colonization of plant growth promoting rhizobacteria (PGPR) in the rhizosphere is an initial and compulsory step in the protection of plants from soil-borne pathogens. Therefore, it is necessary to evaluate the role of root exudates in the colonization of PGPR. Banana root exudates were analyzed by high pressure liquid chromatography (HPLC) which revealed exudates contained several organic acids (OAs) including oxalic, malic and fumaric acid. The chemotactic response and biofilm formation of Bacillus amyloliquefaciens NJN-6 were investigated in response to OA's found in banana root exudates. Furthermore, the transcriptional levels of genes involved in biofilm formation, yqxM and epsD, were evaluated in response to OAs via quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Results suggested that root exudates containing the OAs both induced the chemotaxis and biofilm formation in NJN-6. In fact, the strongest chemotactic and biofilm response was found when 50??M of OAs were applied. More specifically, malic acid showed the greatest chemotactic response whereas fumaric acid significantly induced biofilm formation by a 20.7-27.3% increase and therefore biofilm formation genes expression. The results showed banana root exudates, in particular the OAs released, play a crucial role in attracting and initiating PGPR colonization on the host roots.
Project description:The rhizosphere is an essential pathway for the uptake of metal-based nanoparticles (MNPs) by plant roots. However, the interaction between root exudates and MNPs is still unclear. In this study, we initially identified the major low-molecular-weight organic acids (LMWOAs) in the rice root exudates using hydroponics. Then, the individual LMWOAs were added to CuO nanoparticle suspensions to investigate their effects on the environmental behavior of the MNPs. The results showed that both the variety and the concentration of LMWOAs impacted the aggregation, sedimentation, and dissolution of CuO nanoparticles (NPs). Almost all LMWOAs except succinic acid inhibited the aggregation of CuO NPs by enhancing the electrostatic repulsive force between NPs. The presence of citric and oxalic acids rather than lactic acid greatly improved the stability of CuO NP suspensions, but other acids showed a low promoting and high inhibiting effect on NP sedimentation. Moreover, all the LMWOAs from root exudates facilitated the dissolution of CuO NPs with a positive dose-dependent correlation, especially formic acid. Notably, citric acid, as the most abundant LMWOAs in rice root exudates, largely determined the aggregation, sedimentation, and dissolution of CuO NPs. This study provides a better understanding on NP-plant interactions in the rhizosphere.
Project description:Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
Project description:Bacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated.Maize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates.Enhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain's potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain.
Project description:Australian native species grow competitively in nutrient limited environments, particularly in nitrogen (N) limited soils; however, the mechanism that enables this is poorly understood. Biological nitrification inhibition (BNI), which is the release of root exudates into the plant rhizosphere to inhibit the nitrification process, is a hypothesized adaptive mechanism for maximizing N uptake. To date, few studies have investigated the temporal pattern and components of root exudates by Australian native plant species for BNI. This study examined root exudates from two Australian native species, Hibiscus splendens and Solanum echinatum, and contrasted with exudates of Sorghum bicolor, a plant widely demonstrated to exhibit BNI capacity. Root exudates were collected from plants at two, four, and six weeks after transplanting to solution culture. Root exudates contained three types of organic acids (OAs), oxalic, citric and succinic acids, regardless of the species. However, the two Australian natives species released larger amount of OAs in earlier development stages than S. bicolor. The total quantity of these OAs released per unit root dry mass was also seven-ten times greater for Australian native plant species compared to S. bicolor. The root exudates significantly inhibited nitrification activity over six weeks' growth in a potential nitrification assay, with S. echinatum (ca. 81% inhibition) > S. bicolor (ca. 80% inhibition) > H. splendens (ca. 78% inhibition). The narrow range of BNI capacity in the study plants limited the determination of a relationship between OAs and BNI; however, a lack of correlation between individual OAs and inhibition of nitrification suggests OAs may not directly contribute to BNI. These results indicate that Australian native species generate a strongly N conserving environment within the rhizosphere up to six weeks after germination, establishing a competitive advantage in severely N limited environments.
Project description:C4-dicarboxylic acids, including malic acid, fumaric acid and succinic acid, are valuable organic acids that can be produced and secreted by a number of microorganisms. Previous studies on organic acid production by Aspergillus carbonarius, which is capable of producing high amounts of citric acid from varieties carbon sources, have revealed its potential as a fungal cell factory. Earlier attempts to reroute citric acid production into C4-dicarboxylic acids have been with limited success.In this study, a glucose oxidase deficient strain of A. carbonarius was used as the parental strain to overexpress a native C4-dicarboxylate transporter and the gene frd encoding fumarate reductase from Trypanosoma brucei individually and in combination. Impacts of the introduced genetic modifications on organic acid production were investigated in a defined medium and in a hydrolysate of wheat straw containing high concentrations of glucose and xylose. In the defined medium, overexpression of the C4-dicarboxylate transporter alone and in combination with the frd gene significantly increased the production of C4-dicarboxylic acids and reduced the accumulation of citric acid, whereas expression of the frd gene alone did not result in any significant change of organic acid production profile. In the wheat straw hydrolysate after 9 days of cultivation, similar results were obtained as in the defined medium. High amounts of malic acid and succinic acid were produced by the same strains.This study demonstrates that the key to change the citric acid production into production of C4-dicarboxylic acids in A. carbonarius is the C4-dicarboxylate transporter. Furthermore it shows that the C4-dicarboxylic acid production by A. carbonarius can be further increased via metabolic engineering and also shows the potential of A. carbonarius to utilize lignocellulosic biomass as substrates for C4-dicarboxylic acid production.
Project description:Magnesium (Mg) deficiency, a widespread yet overlooked problem in agriculture, has been reported to retard plant growth and development, through affecting key metabolic pathways. However, the metabolic responses of plant to Mg deficiency is still not fully understood. Here we report a metabolomic study to evaluate the metabolic responses to Mg deficiency in soybean leaves and roots. Hydroponic grown soybean were exposed to Mg starvation for 4 and 8 days, respectively. Metabolic changes in the first mature trifoliolate leaves and roots were quantified by conducting GC-TOF-MS based metabolomic analysis. Principal component analysis (PCA) showed that Mg deficient plants became distinguishable from controls at 4 days after stress (DAS) at metabolic level, and were clearly discriminated at 8 DAS. Mg deficiency could cause large metabolite alterations on carbon and nitrogen metabolism. At 8 DAS, carbon allocation from shoot to root is decreased by Mg deficiency. Remarkably, most amino acids (such as phenylalanine, asparagine, leucine, isoleucine, glycine, glutamine, and serine) showed pronounced accumulation in the leaves, while most organic acids (including pyruvic acid, citric acid, 2-keto-glutaric acid, succinic acid, fumaric acid, and malic acid) were significantly decreased in the roots. Our study shows that the carbon and nitrogen metabolic responses are distinct in leaves and roots under Mg deficiency.
Project description:In this study, thirteen Japanese plum cultivars (Prunus salicina Lindl.) grown under conventional and organic conditions were compared to evaluate the influence of the culture system on bioactive compounds. Their organic acids content (malic, citric, tartaric, succinic, shikimic, ascorbic and fumaric acid), total polyphenols, total anthocyanins, total carotenoids and antioxidant capacity (FRAP, ABTS) were evaluated. The study was performed during two consecutive seasons (2012 and 2013) in two experimental orchards located at the IFAPA centre Las Torres-Tomejil (Seville, SW Spain). The culture system affected all the studied parameters except for total carotenoid content. The organic plums had significantly higher polyphenol and anthocyanin concentrations and a greater antioxidant capacity. Additionally, significant differences between cultivars were also found. 'Showtime' and 'Friar' were the cultivars with the highest polyphenol concentration and antioxidant capacity. 'Black Amber' had the highest anthocyanin content and 'Larry Ann' and 'Songold' the highest carotenoid content. 'Sapphire' and 'Black amber' were the cultivars with the highest concentration of ascorbic acid. Our results showed a strong year effect. In conclusion, organic management had an impact on the production of phytochemical compounds in plums.
Project description:The study aimed at detecting 13 organic acids (oxalic acid, maleic acid, citric acid, tartaric acid, malic acid, quinic acid, succinic acid, fumaric acid, formic acid, acetic acid, propionic acid, isobutyric acid, and butyric acid) by establishing a high-performance liquid chromatography (HPLC). The analysis was performed using two sugar columns, i.e., SH1011 column and KC-811 column. The optimal conditions were as follows: 4?mmol/L HClO4 solution as the eluent with UV-visible detector (210?nm), a flow rate of 1?mL/min at the temperature of 60°C, and the injection volume at 10??L. The results showed that all the calibration curves had excellent linearity (R 2 > 0.9991) within the test ranges. The RSD values of the thirteen analytes were lower than 2.94% at three levels, the recoveries were 91.9%-102.0%, the limit of detection (LOD) was between 0.05 and 10.63??g/mL, and the quantification (LOQ) was between 0.10 and 19.53??g/mL. Finally, the proposed methodology was successfully applied for the analysis of organic acids in the culture medium of edible fungi. In conclusion, the study findings proved that the method was sensitive, accurate, reproducible, and could be readily applied to analyze the organic acids in the samples.
Project description:The aim of the study was to (i) investigate the potential of edible mushroom Boletus badius (Fr.) Fr. to accumulate 53 elements from unpolluted acidic sandy soil and polluted alkaline flotation tailing sites in Poland, (ii) to estimate the low-molecular-weight organic acid (LMWOA) profile and contents in fruit bodies, and finally (iii) to explore the possible relationship between elements and LMWOA content in mushrooms. The content of most elements in fruiting bodies collected from the flotation tailings was significantly higher than in mushrooms from the unpolluted soils. The occurrence of elements determined in fruiting bodies of B. badius has been varied (from 0.01 mg kg-1 for Eu, Lu, and Te up to 18,932 mg kg-1 for K). The results established the high importance of element contents in substrate. Among ten organic acids, nine have been found in wide range: from below 0.01 mg kg-1 for fumaric acid to 14.8 mg g-1 for lactic acid. Lactic and succinic acids were dominant in both areas, and citric acid was also in high content in polluted area. The correlation between element contents and the individual and total content of LMWOAs was confirmed.