Isoxazolin-5-ones and Amino Acids in Root Exudates of Pea and Sweet Pea Seedlings

Direct introduction MALDI FTICR MS based on dried droplet deposition applied to non-targeted metabolomics on Pisum Sativum root exudates

Non-targeted metabolomic approaches based on direct introduction (DI) through a soft ionization source are nowadays used for large-scale analysis and wide cover-up of metabolites in complex matrices. When coupled with ultra-high-resolution Fourier-Transform ion cyclotron resonance (FTICR MS), DI is generally performed through electrospray (ESI), which, despite the great analytical throughput, can suffer of matrix effects due to residual salts or charge competitors. In alternative, matrix assisted laser desorption ionization (MALDI) coupled with FTICR MS offers relatively high salt tolerance but it is mainly used for imaging of small molecule within biological tissues. In this study, we report a systematic evaluation on the performance of direct introduction ESI and MALDI coupled with FTICR MS applied to the analysis of root exudates (RE), a complex mixture of metabolites released from plant root tips and containing a relatively high salt concentration. Classic dried droplet deposition followed by screening of best matrices and ratio allowed the selection of high ranked conditions for non-targeted metabolomics on RE. Optimization of MALDI parameters led to improved reproducibility and precision. A RE desalted sample was used for comparison on ionization efficiency of the two sources and ion enhancement at high salinity was highlighted in MALDI by spiking desalted solution with inorganic salts. Application of a true lyophilized RE sample exhibited the complementarity of the two sources and the ability of MALDI in the detection of undisclosed metabolites suffering of matrix effects in ESI mode.

Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)

Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilis Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.

Rhizobacteria Mitigate the Negative Effect of Aluminum on Pea Growth by Immobilizing the Toxicant and Modulating Root Exudation

High soil acidity is one of the main unfavorable soil factors that inhibit the growth and mineral nutrition of plants. This is largely due to the toxicity of aluminum (Al), the mobility of which increases significantly in acidic soils. Symbiotic microorganisms have a wide range of beneficial properties for plants, protecting them against abiotic stress factors. This report describes the mechanisms of positive effects of plant growth-promoting rhizobacteria Pseudomonas fluorescens SPB2137 on four pea (Pisum sativum L.) genotypes grown in hydroponics and treated with 80 µM AlCl3. In batch culture, the bacteria produced auxins, possessed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, alkalized the medium and immobilized Al, forming biofilm-like structures and insoluble phosphates. Inoculation with Ps. fluorescens SPB2137 increased root and/or shoot biomass of Al-treated plants. The bacteria alkalized the nutrient solution and transferred Al from the solution to the residue, which contained phosphorus that was exuded by roots. As a result, the Al concentration in roots decreased, while the amount of precipitated Al correlated negatively with its concentration in the solution, positively with the solution pH and negatively with Al concentration in roots and shoots. Treatment with Al induced root exudation of organic acids, amino acids and sugars. The bacteria modulated root exudation via utilization and/or stimulation processes. The effects of Al and bacteria on plants varied depending on pea genotype, but all the effects had a positive direction and the variability was mostly quantitative. Thus, Ps. fluorescens SPB2137 improved the Al tolerance of pea due to immobilization and exclusion of toxicants from the root zone.

Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Cyanobacteria are an ancient clade of photosynthetic prokaryotes, whose worldwide occurrence, especially in water, presents health hazards to humans and animals due to the production of a range of toxins (cyanotoxins). These include the sometimes co-occurring, non-encoded diaminoacid neurotoxins 2,4-diaminobutanoic acid (2,4-DAB) and its structural analogue β-N-methylaminoalanine (BMAA). Knowledge of the biosynthetic pathway for 2,4-DAB, and its role in cyanobacteria, is lacking. The aspartate 4-phosphate pathway is a known route of 2,4-DAB biosynthesis in other bacteria and in some plant species. Another pathway to 2,4-DAB has been described in Lathyrus species. Here, we use bioinformatics analyses to investigate hypotheses concerning 2,4-DAB biosynthesis in cyanobacteria. We assessed the presence or absence of each enzyme in candidate biosynthesis routes, the aspartate 4-phosphate pathway and a pathway to 2,4-DAB derived from S-adenosyl-L-methionine (SAM), in 130 cyanobacterial genomes using sequence alignment, profile hidden Markov models, substrate specificity/active site identification and the reconstruction of gene phylogenies. In the aspartate 4-phosphate pathway, for the 18 species encoding diaminobutanoate-2-oxo-glutarate transaminase, the co-localisation of genes encoding the transaminase with the downstream decarboxylase or ectoine synthase - often within hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) clusters, NRPS-independent siderophore (NIS) clusters and incomplete ectoine clusters - is compatible with the hypothesis that some cyanobacteria use the aspartate 4-phosphate pathway for 2,4-DAB production. Through this route, in cyanobacteria, 2,4-DAB may be functionally associated with environmental iron-scavenging, via the production of siderophores of the schizokinen/synechobactin type and of some polyamines. In the pathway to 2,4-DAB derived from SAM, eight cyanobacterial species encode homologs of SAM-dependent 3-amino-3-carboxypropyl transferases. Other enzymes in this pathway have not yet been purified or sequenced. Ultimately, the biosynthesis of 2,4-DAB appears to be either restricted to some cyanobacterial species, or there may be multiple and additional routes, and roles, for the synthesis of this neurotoxin.

Metabolic solutions to the biosynthesis of some diaminomonocarboxylic acids in nature: Formation in cyanobacteria of the neurotoxins 3-N-methyl-2,3-diaminopropanoic acid (BMAA) and 2,4-diaminobutanoic acid (2,4-DAB)

The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown. This review considers possible metabolic routes, by analogy with reactions used in other species, by which these amino acids might be biosynthesised by cyanobacteria, which are a widespread potential environmental source of these neurotoxins. Where possible, the gene expression that might be implicated in these biosyntheses is discussed.

A tale of four kingdoms – isoxazolin-5-one- and 3-nitropropanoic acid-derived natural products

The occurrence, structural diversity, (bio-)synthesis, properties and detoxification mechanisms of isoxazolinone- and 3-nitropropanoic acid-derived natural compounds are reviewed.

Key roles of microsymbiont amino acid metabolism in rhizobia-legume interactions

Rhizobia are bacteria in the α-proteobacterial genera Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium and Bradyrhizobium that reduce (fix) atmospheric nitrogen in symbiotic association with a compatible host plant. In free-living and/or symbiotically associated rhizobia, amino acids may, in addition to their incorporation into proteins, serve as carbon, nitrogen or sulfur sources, signals of cellular nitrogen status and precursors of important metabolites. Depending on the rhizobia-host plant combination, microsymbiont amino acid metabolism (biosynthesis, transport and/or degradation) is often crucial to the establishment and maintenance of an effective nitrogen-fixing symbiosis and is intimately interconnected with the metabolism of the plant. This review summarizes past findings and current research directions in rhizobial amino acid metabolism and evaluates the genetic, biochemical and genome expression studies from which these are derived. Specific sections deal with the regulation of rhizobial amino acid metabolism, amino acid transport, and finally the symbiotic roles of individual amino acids in different plant-rhizobia combinations.

The short-term effect of cadmium on low molecular weight organic acid and amino acid exudation from mangrove (Kandelia obovata (S., L.) Yong) roots

The aim of this study was to evaluate short-term concentration and time effects of cadmium on Kandelia obovata (S., L.) Yong root exudation, thereby evaluating and predicting the ecophysiological effects of mangrove to heavy metals at the root level. Mature K. obovata propagules were cultivated in a sandy medium for 3 months, and then six concentrations of Cd (0, 2.5, 5, 10, 20, and 40 mg L(-1)) were applied. After exposure time of 24 h and 7 days, respectively, the root exudates of K. obovata were collected and low molecular weight organic acids (LMWOAs) and amino acids of which were analyzed. In addition, we measured glutathione, soluble protein content, and Cd concentration in the plant. We found 10 and 15 types of LMWOAs and amino acids in root exudates of K. obovata with total concentrations ranging from 29.54 to 43.08 mg g(-1) dry weight (DW) roots and from 737.35 to 1,452.46 ng g(-1) DW roots, respectively. Both of them varied in quality and quantity under different Cd treatment strengths and exposure times. Oxalic, acetic, L-malic, tartaric acid, tyrosine, methionine, cysteine, isoleucine, and arginine were dominant. Both LMWOAs and amino acids excreted from K. obovata roots play a key role in Cd toxicity resistance. The responsiveness of amino acids was less than that of LMWOAs. We suggest that the ecological effect of root-excreted free amino acids in the rhizosphere is mainly based on the role of nutrients, supplemented with detoxification to heavy metals.

Slantingly cross loading sample system enables simultaneous performance of separation and mixture to detect molecular interactions on thin-layer chromatography

Anthocyanins are major flower pigments that can be affected by copigments, colorless compounds that can modify anthocyanin coloration to more intense and bluer. Thin-layer chromatography (TLC) is an available technique to separate and analyze anthocyanins and copigments. To easily and comprehensively detect copigments, we added function of mixture of compounds to TLC; by slantingly cross loading samples on TLC, compounds are symmetrically developed at various angle lines from the upper origin to individual R(f) values and cross each other in an orderly fashion, where mixture is simultaneously performed with separation. Occurrence of copigments can be detected as a coloration change on the developed line of anthocyanin. Pink sweet pea (Lathyrus odoratus L.) petals were analyzed by the cross-TLC and a more intense spot and a paler spot on the anthocyanin line were detected. As each spot overlapped with an ultraviolet absorbance line, each of these ultraviolet absorption compounds was purified and identified as kaempferol 3-rhamnoside and 2-cyanoethyl-isoxazolin-5-one, respectively. Whereas kaempferol 3-rhamnoside is a flavonoid and had a general copigment effect of more intense and bluer coloration change, 2-cyanoethyl-isoxazolin-5-one is a compound whose structure is outside of conventional categories of copigments and had a novel effect to change anthocyanin coloration paler while maintaining color tone. We determined that the search for copigments should be carried out without pre-existing prediction of structures and effects. We have shown that slantingly cross loading samples system on plate-type chromatography is an effective technique for such comprehensive analysis of molecular interaction.

Expression of the nodulation gene nodA in Rhizobium meliloti and localization of the gene product in the cytosol

The nodA gene of Rhizobium meliloti encodes a 21.8-kDa protein, which is conserved in several Rhizobium species. We overproduced the nodA protein as a fusion product with a portion of the lambda cI repressor in Escherichia coli. This fusion protein was purified from inclusion bodies by gel and hydroxyapatite chromatography in the presence of NaDodSO(4). Monospecific polyclonal antibodies against the hybrid protein were used to detect the nodA protein in the cytosol of E. coli and R. meliloti by immunoblotting. In contrast to experiments with antibodies against the R. meliloti nodC membrane protein, the alfalfa-R. meliloti nodulation was not affected by the addition of anti-nodA antibodies to medium and inoculum. This suggests that the nodA protein is located within the cell and is therefore not accessible to antibodies. The expression of the nodA gene is induced in R. meliloti by various compounds present in the exudate of leguminous plants, particularly by the flavone luteolin. We show that the plant hormone trigonelline also has some inducing activity. The nodC protein was further localized in the membrane fraction of R. meliloti. Our experiments demonstrate that the nodC transmembrane protein is not necessary for the uptake of the compounds inducing the synthesis of the nodA protein. The nodA and the nodC proteins were also detected in mature nodules. During nodule development, the nodC protein may be processed to a 34-kDa protein.

The supernumerary chromosome of Nectria haematococca that carries pea-pathogenicity-related genes also carries a trait for pea rhizosphere competitiveness

Fungi are found in a wide range of environments, and the ecological and host diversity of the fungus Nectria haematococca has been shown to be due in part to unique genes on different supernumerary chromosomes. These chromosomes have been called "conditionally dispensable" (CD) since they are not needed for axenic growth but are important for expanding the host range of individual isolates. From a biological perspective, the CD chromosomes can be compared to bacterial plasmids that carry unique genes that can define the habits of these microorganisms. The current study establishes that the N. haematococca PDA1-CD chromosome, which contains the genes for pea pathogenicity (PEP cluster) on pea roots, also carries a gene(s) for the utilization of homoserine, a compound found in large amounts in pea root exudates. Competition studies demonstrate that an isolate that lacks the PEP cluster but carries a portion of the CD chromosome which includes the homoserine utilization (HUT) gene(s) is more competitive in the pea rhizosphere than an isolate without the CD chromosome.

Microbial dynamics and interactions in the spermosphere

The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.

Identification and quantification of natural isoxazolinone compounds by capillary zone electrophoresis

A capillary zone electrophoresis (CZE) method that is specific, simple, rapid and also cheap was developed to analyse some natural UV-absorbing isoxazolinone compounds with toxic potential present in legume seedlings. The six most common natural isoxazolinone compounds were separated within 10 min with 25 mM potassium phosphate (pH 7.5) containing 8% 1-propanol as running buffer. A 60 cm coated fused-silica capillary (52.6 cm effective length x 75 microm I.D.), with an electric field of 375 V/cm at 30 degrees C was used. The limit of detection ranged from 0.01 mM (3.0 microg/ml) to 0.03 mM (7.7 microg/ml). Linearity between peak areas and concentrations ranging from 0.05 mM to 1.75 mM were determined for each isoxazolinone. The correlation coefficient was 0.9954 or greater. Both relative migration time and peak area were reproducible. The RSD of relative migration time is between 0.44 and 1.94% and RSD of peak area is between 1.26 and 6.86%. The concentrations of isoxazolinones in Lathyrus odoratus and L. sativus seedlings obtained by CZE were in agreement with the previous results from HPLC.

Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source

Plant roots secrete a complex polysaccharide mucilage that may provide a significant source of carbon for microbes that colonize the rhizosphere. High molecular weight mucilage was separated by high-pressure liquid chromatography gel filtration from low molecular weight components of pea root exudate. Purified pea root mucilage generally was similar in sugar and glycosidic linkage composition to mucilage from cowpea, wheat, rice, and maize, but appeared to contain an unusually high amount of material that was similar to arabinogalactan protein. Purified pea mucilage was used as the sole carbon source for growth of several pea rhizosphere bacteria, including Rhizobium leguminosarum 8401 and 4292, Burkholderia cepacia AMMD, and Pseudomonas fluorescens PRA25. These species grew on mucilage to cell densities of three- to 25-fold higher than controls with no added carbon source, with cell densities of 1 to 15% of those obtained on an equal weight of glucose. Micromolar concentrations of nod gene-inducing flavonoids specifically stimulated mucilage-dependent growth of R. leguminosarum 8401 to levels almost equaling the glucose controls. R. leguminosarum 8401 was able to hydrolyze p-nitrophenyl glycosides of various sugars and partially utilize a number of purified plant polysaccharides as sole carbon sources, indicating that R. leguminosarum 8401 can make an unexpected variety of carbohydrases, in accordance with its ability to extensively utilize pea root mucilage.

Toxins in the seedlings of some varieties of grass pea (Lathyrus sativus)

The major toxin present in the dry seeds and seedlings of Lathyrus sativus is the neurotoxin 3-N-oxalyl-L-2,3-diaminopropanoic acid (beta-ODAP). The presence of one additional neurotoxin and an osteotoxin in the seedlings increases the overall toxicity. Isolation, purification, and detection of these toxins are described.

Genetic analysis of a region of the Rhizobium meliloti pSym plasmid specifying catabolism of trigonelline, a secondary metabolite present in legumes

Genes controlling the catabolism of trigonelline, a secondary metabolite that is often present in legumes, are located on the pSym megaplasmid of Rhizobium meliloti. To investigate the role of bacterial trigonelline catabolism in the Rhizobium-legume symbiosis, we identified and characterized the R. meliloti RCR2011 genetic loci (trc) controlling trigonelline catabolism. Tn5-B20 mutagenesis showed that the trc region is a continuous DNA segment of 9 kb located 4 kb downstream of the nifAB and fdxN genes. Trc mutants fell into two classes according to their phenotype and location: (i) mutants carrying Tn5-B20 insertions in the right-hand part of the trc region were incapable of growing on trigonelline as the sole carbon and/or nitrogen source, and (ii) insertions in the left-hand part of the trc region resulted in delayed growth on trigonelline as the sole carbon and/or nitrogen source. No significant defect in nodule formation or nitrogen fixation was detected for mutants of either class. Screening of a set of R. meliloti strains from various geographical origins showed that all of these strains are able to catabolize trigonelline and show sequence homology between their megaplasmids and a trc probe.

Rhizobium meliloti Genes Encoding Catabolism of Trigonelline Are Induced under Symbiotic Conditions

Rhizobium meliloti trc genes controlling the catabolism of trigonelline, a plant secondary metabolite often abundant in legumes, are closely linked to nif-nod genes on the symbiotic megaplasmid pSym [Boivin, C., Malpica, C., Rosenberg, C., Denarie, J., Goldman, A., Fleury, V., Maille, M., Message, B., and Tepfer, D. (1989). In Molecular Signals in the Microbe-Plant Symbiotic and Pathogenic Systems. (Berlin: Springer-Verlag), pp. 401-407]. To investigate the role of trigonelline catabolism in the Rhizobium-legume interaction, we studied the regulation of trc gene expression in free-living and in endosymbiotic bacteria using Escherichia coli lacZ as a reporter gene. Experiments performed with free-living bacteria indicated that trc genes were organized in at least four transcription units and that the substrate trigonelline was a specific inducer for three of them. Noninducing trigonelline-related compounds such as betaines appeared to antagonize the inducing effect of trigonelline. None of the general or symbiotic regulatory genes ntrA, dctB/D, or nodD seemed to be involved in trigonelline catabolism. trc fusions exhibiting a low basal and a high induced [beta]-galactosidase activity when present on pSym were used to monitor trc gene expression in alfalfa tissue under symbiotic conditions. Results showed that trc genes are induced during all the symbiotic steps, i.e., in the rhizosphere, infection threads, and bacteroids of alfalfa, suggesting that trigonelline is a nutrient source throughout the Rhizobium-legume association.

Plant-plant interactions

Higher plants show three types of biochemical adaptation which enable them to combat pathogenic organisms in the form of lower plants. Firstly they may synthesize antibacterial or antifungal compounds in concentrations that prevent the invasion of the higher plant by the bacteria or fungi. Secondly they may synthesize such compounds in less than adequate amounts for defence in healthy tissues but respond to invasion by increasing the synthesis; and, thirdly, they may respond to invasion by synthesizing antibacterial or antifungal compounds de novo. Higher plants also show biochemical adaptations that enable them to compete with individuals of the same or different higher plant species. These include the synthesis of volatile and water-soluble phytotoxins which suppress the germination, growth, or both, of competitors.