Browsing by Subject "Transcriptome analysis"

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Transcriptional profiling of Bacillus amyloliquefaciens FZB42 in response to seed and root exudates collected under different nutrient regimes
(2010) Carvalhais Costa, Lilia; von Wirén, Nicolaus
Plant growth-promoting rhizobacteria (PGPR) live in close association with plants and improve their growth. Bacillus amyloliquefaciens strain FZB42 is a prominent plant root-colonizing bacterium that is able to stimulate the growth of maize. To decipher the molecular cross-talk between B. amyloliquefaciens and crop plants, an exploratory analysis of the effect of seed and root exudates on the transcriptome of Bacillus amyloliquefaciens FZB42 was performed. Root exudates were collected from maize plants grown in an axenic hydroponic system under nutrient sufficiency or under deficient supply of nitrogen (N), phosphorus (P), iron (Fe) or potassium (K). An analysis of primary metabolites in the exudates was carried out, compared between treatments, and correlated with the transcriptional profiles of Bacillus amyloliquefaciens FZB42 that were gained after incubation of the bacterial culture with the root exudates. Higher exudation rates of citrate were found under Fe deficiency and greater release of ã-amino butyric acid under P deficiency. Based on a negative correlation observed between the average diffusion coefficient of N, P, K, and Fe in soils and the exudation rates of primary metabolites under conditions of N, P, K, or Fe deficiency, it was hypothesized that the exudation of sugars, amino acids and organic acids may reflect the availability and mobility of plant nutrients in soils. In the presence of seed and root exudates collected from nutrient-sufficient plants, genes involved in spore germination, transport and utilization of nutrients, biosynthesis pathways, multidrug transporters, motility and competence development were differentially expressed. In comparison to P, Fe and K, N-deficient maize root exudates caused a more distinguished change in the transcriptome of bacteria when they were in the logarithmic growth phase. During this growth phase, a number of genes coding for ribosomal proteins were down-regulated by N-deficient maize root exudates, indicating that bacterial activity was repressed. Exclusively in the presence of P-deficient maize root exudates, several genes associated to bacterial motility were induced. Moreover, a gene involved in the biosynthesis of the auxin precursor tryptophan was up-regulated by all deficiency treatments. In the transitional growth phase of Bacillus amyloliquefaciens FZB42, several genes were commonly down-regulated in different deficiency treatments. This finding is in agreement with previous studies showing that quorum-sensing and starvation-sensing are integrated to regulate cell entry into the transient phase. Taken together, this is the first study comparing the effect of different nutrient deficiencies on the composition of primary metabolites in root exudates of one plant species and evaluating systematically the transcriptional response of a Gram-positive PGPR to seed and root exudates collected from plants grown under different nutrient regimes. This analysis provides new information about the early communication between plant roots and PGPR and points to involved genes and processes that merit further investigation.
Transcriptomics and hormonal regulation of cluster root development in phosphate-deficient white lupin
(2014) Wang, Zhengrui; Neumann, Günter
Among crops, white lupin (Lupinus albus) represents the extraordinary ability to acquire sparingly soluble soil phosphate (Pi) by formation of cluster roots (CRs), mediating intense exudation of phosphorus (P)-mobilising root exudates (citrate, phenolics, protons and acid phosphatase). It is widely used as a model plant for investigations of P acquisition by root-induced chemical modifications of the rhizosphere. During the last two decades, a large pool of information on CR function and physiology was obtained mainly by hypothesis-driven research. Based on these findings, this study was designed to get a more comprehensive picture of the metabolic changes during CR development using a transcriptome sequencing approach. The outcome of the transcriptome analysis was the basis for the formulation of research questions on the regulation of CR formation and function to be investigated more in detail: Chapter I, focuses on transcriptome sequencing used for the first time for a systematic comparison of different stages in CR development. To get insights into the regulatory factors involved in CR formation, special emphasis was placed on hormone-related genes. Initiation of CR primordia in the pre-emergent (PE) zone was reflected by strongest expression of genes involved in transport and biosynthesis of auxins, brassinosteroids (BRs) and cytokinin receptors. Cluster root maturation, involving meristem degeneration and root hair proliferation was associated with strongly increased expression of ethylene-related transcripts and decreased expression of auxin- and BR-related genes. Also transcripts related with abscisic and jasmonic acids and cytokinin degradation were up-regulated in mature (MA) clusters. The primary metabolism, highly expressed in juvenile (JU) clusters, underwent significant modifications during CR maturation with increased contribution of Pi-independent bypass reactions, promoting biosynthesis of organic acids. Citrate catabolism and respiration were down-regulated, triggering citrate accumulation in MA clusters. Up-regulation of phenylpropanoid pathways reflected accumulation of phenolics. Increased expression of transcripts encoding ALMT and MATE transporters may be involved in the exudation of flavonoids and citrate, while up-regulation of transcripts encoding Pi transporters mediates subsequent uptake of mobilised Pi. Predominant expression of nucleotide degradation and secretory acid phosphatase in MA clusters coincides with Pi re-translocation and mobilisation of organic soil P. Up-regulation of the FIT transcription factor, usually mediating the expression of Fe deficiency responses (root hair proliferation, proton extrusion, Fe(III)-reduction, exudation of phenolics) can be observed also in MA clusters of P-deficient Lupinus albus even under Fe-sufficient conditions. This raises the question, whether FIT has a similar function in the regulation of P deficiency responses. Chapter II, addresses the question whether sucrose acts as a shoot-borne signal for CR formation. External sucrose amendments to P-sufficient plants, at concentrations similar to those in PE root zones of P-deficient plants, induced CR formation comparable to P-deficient plants. Palatinose (25 mM), and combined application of glucose/fructose (both at 12.5 mM) failed to induce CR formation under P-sufficient conditions, demonstrating a specific signal function of sucrose and excluding osmotic and carbon source effects. However, CRs induced by sucrose were not functional with respect to citrate exudation, acid phosphatase and phosphoenolpyruvate carboxylase (PEPC) activities and expression of related genes (LaMATE, LaSAP and LaPEPC) quantified by RT-qPCR. In Chapter III, the interactions of different phytohormones and sucrose on CR formation were investigated more in detail by an integrated approach of RT-qPCR, hormone translocation analyses and exogenous application of hormones or hormone antagonists. Shoot-to-root translocation of auxin was unaffected by P limitation, supporting the hypothesis that sucrose, rather than auxins, acts as major shoot-borne signal, triggering the induction of CR primordia. Ethylene may act as mediator of the sucrose signal, as indicated by strong inhibitory effects of the ethylene antagonist CoCl2 on CR formation induced by sucrose or P limitation. As reported in other plant species, moderately increased production of ethylene and brassinosteroids (BRs) may induce biosynthesis and transport of root-borne auxins, indicated by increased expression of respective genes (YUCCA, PIN1, AUX1, BR, ACC_oxidase) in pre-emergent clusters. A role of BR in CR formation is further underlined by inhibitory effects of BR antagonists. The well-documented inhibition of root elongation by high doses of ethylene may be involved in the inhibition of lateral rootlets growth during CR maturation, indicated by a massive increase of gene expression involved in ethylene production, associated with decline of transcripts with stimulatory effects (BR- and auxin-related genes). Based on these findings, models for the regulatory networks involved in CR formation (Chapter III) and function (Chapter I) have been developed.