SEARCH · PubMed Health

Results for “root exudates”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources

PubMed1999

Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of spartina alterniflora

The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons by molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rates and geochemical parameters. SO42- reduction was rapid in marsh sediments with rates up to 3.5 &mgr;mol ml-1 day-1. Rates increased greatly when plant growth began in April and decreased again when plants flowered in late July. Results with nucleic acid probes revealed that SRB rRNA accounted for up to 43% of the rRNA from members of the domain Bacteria in marsh sediments, with the highest percentages occurring in bacteria physically associated with root surfaces. The relative abundance (RA) of SRB rRNA in whole-sediment samples compared to that of Bacteria rRNA did not vary greatly throughout the year, despite large temporal changes in SO42- reduction activity. However, the RA of root-associated SRB did increase from <10 to >30% when plants were actively growing. rRNA from members of the family Desulfobacteriaceae comprised the majority of the SRB rRNA at 3 to 34% of Bacteria rRNA, with Desulfobulbus spp. accounting for 1 to 16%. The RA of Desulfovibrio rRNA generally comprised from <1 to 3% of the Bacteria rRNA. The highest Desulfobacteriaceae RA in whole sediments was 26% and was found in the deepest sediment samples (6 to 8 cm). Culturable SRB abundance, determined by most-probable-number analyses, was high at >10(7) ml-1. Ethanol utilizers were most abundant, followed by acetate utilizers. The high numbers of culturable SRB and the high RA of SRB rRNA compared to that of Bacteria rRNA may be due to the release of SRB substrates in plant root exudates, creating a microbial food web that circumvents fermentation.

Journal Article↗

PubMed2005

Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest.

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

Ascomycota↗

PubMed2006

Diverse flavonoids stimulate NodD1 binding to nod gene promoters in Sinorhizobium meliloti.

NodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium Sinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressed nodD genes from different species of rhizobia in a strain of S. meliloti lacking endogenous NodD activity. We observed that nod gene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity of S. meliloti NodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding to nod gene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulate nod gene expression in S. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 to nod gene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes at nod gene promoters but that only luteolin is capable of promoting the downstream changes necessary for nod gene induction.

Bacterial Proteins↗

PubMed1987

Flavonoids induce Rhizobium leguminosarum to produce nodDABC gene-related factors that cause thick, short roots and root hair responses on common vetch.

Rhizobium leguminosarum produced a factor(s) that caused thick, short roots (Tsr phenotype) as well as root hair induction (Hai phenotype) and deformation (Had phenotype) in Vicia sativa plants upon incubation with root exudate or with one of the nod gene inducers naringenin or apigenin; this was a nodDABC gene-dependent process. Detection of the Hai and Had phenotypes was much more sensitive than that of the Tsr phenotype.

Fabaceae↗

PubMed1993

Multiple copies of nodD in Rhizobium tropici CIAT899 and BR816.

Rhizobium tropici strains are able to nodulate a wide range of host plants: Phaseolus vulgaris, Leucaena spp., and Macroptilium atropurpureum. We studied the nodD regulatory gene for nodulation of two R. tropici strains: CIAT899, the reference R. tropici type IIb strain, and BR816, a heat-tolerant strain isolated from Leucaena leucocephala. A survey revealed several nodD-hybridizing DNA regions in both strains: five distinct regions in CIAT899 and four distinct regions in BR816. Induction experiments of a nodABC-uidA fusion in combination with different nodD-hybridizing fragments in the presence of root exudates of the different hosts indicate that one particular nodD copy contributes to nodulation gene induction far more than any other nodD copy present. The nucleotide sequences of both nodD genes are reported here and show significant homology to those of the nodD genes of other rhizobia and a Bradyrhizobium strain. A dendrogram based on the protein sequences of 15 different NodD proteins shows that the R. tropici NodD proteins are linked most closely to each other and then to the NodD of Rhizobium phaseoli 8002.

Amino Acid Sequence↗

PubMed2004

The davDT operon of Pseudomonas putida, involved in lysine catabolism, is induced in response to the pathway intermediate delta-aminovaleric acid.

Pseudomonas putida KT2440 is a soil microorganism that attaches to seeds and efficiently colonizes the plant's rhizosphere. Lysine is one of the major compounds in root exudates, and P. putida KT2440 uses this amino acid as a source of carbon, nitrogen, and energy. Lysine is channeled to delta-aminovaleric acid and then further degraded to glutaric acid via the action of the davDT gene products. We show that the davDT genes form an operon transcribed from a single sigma70-dependent promoter. The relatively high level of basal expression from the davD promoter increased about fourfold in response to the addition of exogenous lysine to the culture medium. However, the true inducer of this operon seems to be delta-aminovaleric acid because in a mutant unable to metabolize lysine to delta-aminovaleric acid, this compound, but not lysine, acted as an effector. Effective induction of the P. putida P(davD) promoter by exogenously added lysine requires efficient uptake of this amino acid, which seems to proceed by at least two uptake systems for basic amino acids that belong to the superfamily of ABC transporters. Mutants in these ABC uptake systems retained basal expression from the davD promoter but exhibited lower induction levels in response to exogenous lysine than the wild-type strain.

Amino Acids, Neutral↗

PubMed2006

Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen Ralstonia solanacearum.

Ralstonia solanacearum, a soilborne plant pathogen of considerable economic importance, invades host plant roots from the soil. Qualitative and quantitative chemotaxis assays revealed that this bacterium is specifically attracted to diverse amino acids and organic acids, and especially to root exudates from the host plant tomato. Exudates from rice, a nonhost plant, were less attractive. Eight different strains from this heterogeneous species complex varied significantly in their attraction to a panel of carbohydrate stimuli, raising the possibility that chemotactic responses may be differentially selected traits that confer adaptation to various hosts or ecological conditions. Previous studies found that an aflagellate mutant lacking swimming motility is significantly reduced in virulence, but the role of directed motility mediated by the chemotaxis system was not known. Two site-directed R. solanacearum mutants lacking either CheA or CheW, which are core chemotaxis signal transduction proteins, were completely nonchemotactic but retained normal swimming motility. In biologically realistic soil soak virulence assays on tomato plants, both nonchemotactic mutants had significantly reduced virulence indistinguishable from that of a nonmotile mutant, demonstrating that directed motility, not simply random motion, is required for full virulence. In contrast, nontactic strains were as virulent as the wild-type strain was when bacteria were introduced directly into the plant stem through a cut petiole, indicating that taxis makes its contribution to virulence in the early stages of host invasion and colonization. When inoculated individually by soaking the soil, both nontactic mutants reached the same population sizes as the wild type did in the stems of tomato plants just beginning to wilt. However, when tomato plants were coinoculated with a 1:1 mixture of a nontactic mutant and its wild-type parent, the wild-type strain outcompeted both nontactic mutants by 100-fold. Together, these results indicate that chemotaxis is an important trait for virulence and pathogenic fitness in this plant pathogen.

Chemotaxis↗

PubMed1995

The Rhizobium-plant symbiosis.

Rhizobium, Bradyrhizobium, and Azorhizobium species are able to elicit the formation of unique structures, called nodules, on the roots or stems of the leguminous host. In these nodules, the rhizobia convert atmospheric N2 into ammonia for the plant. To establish this symbiosis, signals are produced early in the interaction between plant and rhizobia and they elicit discrete responses by the two symbiotic partners. First, transcription of the bacterial nodulation (nod) genes is under control of the NodD regulatory protein, which is activated by specific plant signals, flavonoids, present in the root exudates. In return, the nod-encoded enzymes are involved in the synthesis and excretion of specific lipooligosaccharides, which are able to trigger on the host plant the organogenic program leading to the formation of nodules. An overview of the organization, regulation, and function of the nod genes and their participation in the determination of the host specificity is presented.

Base Sequence↗

PubMed1976

Zoospore chemotaxis in Australian isolates of Phytophthora species.

Zoospores of Australian isolates of Phytophthora drechsleri, P. cryptogea, P. cinnamomi, P. nicotianae var. parasitica, and P. citricola were examined for their chemotactic responses to asparagine, glutamine, aspartate, glutamate, and structurally related compounds. Structural requirements for attraction include the alpha-amino-acid group with a short carbon chain terminating in an amide group. The one American isolate tested gave a different result and possible reasons for this are discussed. The pH of the environment was important, a neutral-charged molecule was more attractive than a negatively charged molecule, hence glutamine and aspartate were more attractive at pH 3.0 than pH 5.0. Zoospores tended to move away from regions with a high hydrogen ion concentration. Compounds other than amino acids were slightly attractive including several sugars and ethanol. Synergistic interactions between amino acids, ethanol, and sucrose were observed and may account for the high levels of attraction of zoospores to root exudates and extracts.

Amino Acids↗

PubMed1980

Interaction of lectins from soybean and peanut with rhizobia that nodulate soybean, peanut, or both plants.

Four of 14 strains of Rhizobium japonicum from soybean nodulated peanut (Arachis hypogaea L. cultivar Jumbo Virginia), and 3 of 8 Rhizobium sp. strains from peanut nodulate soybean (Glycine max (L.) Merr. cultivar Harosoy 63). Cells of three peanut rhizobia bound fluorescent- and radioisotope-labeled soybean lectin. Two of these strains failed to nodulate soybean, and conversely, two peanut strains that nodulated soybean did not bind to soybean lectin. Both culture medium and age had pronounced effects of the number of peanut rhizobia cells that bound fluorescent-labeled soybean lectin. Harosoy 63 soybean root exudates stimulated the growth of peanut rhizobia, but had no consistent influence on the number of cells that bound soybean lectin. Although extracellular soybean lectin receptors were present in culture fluids from each of the peanut rhizobia whose cells bound the lectin, the titer of receptors was greatest for strains 3G4b5. The affinity constants for the adherence of soybean lectin to Rhizobium sp. 3G4b5 cells from cultures of various ages ranged from 4.2 X 10(6) to 4.9 X 10(6) M-1, and the number of lectin binding sites per cell decreased as cells aged. Cells of the soybean and peanut rhizobia did not bind fluorescent- or radioisotope-labeled peanut lectin. The results indicate that there is no relationship between the ability of peanut and soybean rhizobia to nodulate the reciprocal host plant and their ability to bind to the lectin of that plant.

Arachis↗

PubMed2004

Environmental modulation of the pssTNOP gene expression in Rhizobium leguminosarum bv. trifolii.

Exopolysaccharide production by Rhizobium leguminosarum bv. trifolii is required for successful establishment of nitrogen-fixing symbiosis with clover (Trifolium pratense L.). Using plasmid-borne transcriptional fusions of promoters of pss genes with promoterless lacZ the effect of root exudate, phosphate, and ammonia on expression of pssT, pssN, pssO, and pssP genes in wild-type strain RtTA1 background was determined. A stimulating effect of these environmental factors on pssO and pssP gene expression was observed. The putative pssO gene promoter was determined to be a strong promoter within which the divergent nod-box element was identified. The pssO promoter was slightly inducible in a flavonoid-dependent manner in wild-type R. leguminosarum bv. trifolii strains RtTA1 and ANU843 and very weakly active in a mutant of strain ANU843 that lacks the regulatory nodD gene. The expression of pssO and pssP genes in planta was investigated using plasmid-borne pssO-gusA and pssP-gusA fusions under different phosphate availability to clover. The level of pssO-gusA fusion expression was shown to be dependent on phosphate concentration in the plant growth medium.

Artificial Gene Fusion↗

PubMed2004

Influence of substrate composition and flow rate on growth of Azospirillum brasilense Cd in a co-culture with 3 sorghum rhizobacteria.

The ability of Azospirillum brasilense Cd to colonize the niche occupied by 3 bacterial strains previously isolated from sorghum rhizosphere was studied by means of the Biolog system. The isolates were identified by different methods as strains belonging to Pseudomonas putida, Stenotrophomonas maltophilia, and Klebsiella terrigena species. Several C sources, also chosen among the constituents of sorghum root exudates, were used to evaluate the metabolic profiles of Azospirillum and the sorghum rhizobacteria. Azospirillum brasilense Cd exploited the same class of C compounds as the sorghum rhizobacteria and overlapped in their niche requirements. Since structure and functioning of a microbial community are largely affected by the flow rate of nutrient supply, the competitive behavior of A. brasilense Cd was studied in a chemostat mixed culture under C-limited conditions using disodium succinate as C source. Only at high growth rates, i.e., when the C source was highly supplied, A. brasilense Cd appeared to be a good competitor and it became the dominant species, whereas at low growth rates, it was outnumbered by the other species. However, the coexistence of all the strains was always maintained, thus suggesting that interactions other than competition or a potential cross-feeding might occur within the mixed culture.

Amino Acids↗

PubMed2025

Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants↗

PubMedDate not supplied

Modeling carbon and nitrogen transformations for adjustment of compost application with nitrogen uptake by wheat.

Environmentally sound management of the use of composts in agriculture relies on matching the rate of release of available N from compost-amended soils to the crop demand. To develop such management it is necessary to (i) characterize the properties of composts that control their rates of decomposition and release of N and (ii) determine the optimal amount of composts that should be applied annually to wheat (Triticum aestivum L.). Carbon and N mineralization were measured under controlled conditions to determine compost decomposition rate parameters, and the NCSOIL model was used to derive the organic wastes parameters that control the rates of N and C transformations in the soil. We also characterized the effect of a drying period to estimate the effects of the dry season on C and N dynamics in the soil. The optimized compost parameters were then used to predict mineral N concentration dynamics in a soil-wheat system after successive annual applications of compost. Sewage sludge compost (SSC) and cattle manure compost (CMC) mineralization characteristics showed similar partitioning into two components of differing ease of decomposition. The labile component accounted for 16 to 20% of total C and 11 to 14% of total N, and it decomposed at a rate of 2.4 x 10(-2) d(-1), whereas the resistant pool had a decomposition rate constant of 1.2 to 1.4 x 10(-4) d(-1). The main differences between the two composts resulted from their total C and N and inorganic N contents, which were determined analytically. The long-term effect of a drying period on C and N mineralization was negligible. Use of these optimization results in a simulation of compost mineralization under a wheat crop, with a modified plant-effect version of the NCSOIL model, enabled us to evaluate the effects of the following factors on the C and N dynamics in soil: (i) soil temperature, (ii) mineral N uptake by plants, and (iii) release of very labile organic C in root exudates. This labile organic C enhanced N immobilization following application, and so decreased the N available for uptake by plants.

Agriculture↗

PubMed2003

Allelopathy in the natural and agricultural ecosystems and isolation of potent allelochemicals from Velvet bean (Mucuna pruriens) and Hairy vetch (Vicia villosa).

We have studied on allelopathy of plants and developed methods to identify the effective substances in root exudates, leaf leacheate, and volatile chemicals emitted from plants. We found traditional cover plants that show allelopathic activity are useful for weed control. It could eliminate the use of synthetic chemicals for this purpose. Allelopathy is a natural power of plants to protect themselves by producing natural organic chemicals. Some endemic plants in Asia, already known by farmers in the region, as either cover crops used in intercropping, hedgerow, or agroforestry, were found to possess strong allelopathic abilities. Our group identified several allelochemicals from these plants. These allelopathic cover crops, mostly leguminous plants, provide protein rich food, and grow easily without artificial fertilizers, herbicides, insecticides and fungicides. In this regards, these allelopathic cover crops could save food shortage in rural area, and are useful for environmental conservation. Screenings of allelopathic plants by specific bioassays and field tests have been conducted. Hairy vetch (Vicia villosa) and Velvet bean (Mucuna pruriens) are two promising species for the practical application of allelopathy. An amino acid, L-DOPA, unusual in plants, plays an important role as allelochemical in Velvet bean (Mucuna pruriens). Hairy vetch is the most promising cover plant for the weed control in orchard, vegetable and rice production and even for landscape amendment in abandoned field in Japan. We have isolated "cyanamide", a well known nitrogen fertilizer, from Hairy vetch. This is the first finding of naturally produced cyanamide in the world.

Crops, Agricultural↗

PubMedDate not supplied

[The interaction between corn and Burkholderia (Pseudomonas) cepacia].

Burkholderia (Pseudomonas) cepacia is a plant growth promoting rhizobacteria that could improve maize productivity. In this work we studied some properties of B. cepacia strain 0057 in relation to interaction with maize. Spermosphere effect, chemostatic response, indolic compounds and siderophores production were evaluated. We observed inhibitory effect on bacterial growth by maize seeds and their soluble extracts. Root exudates had positive chemiostatic effect. We founded indolic compounds production (20.1 micrograms/ml) and siderophore presence. We think that this microorganisms could improve maize production.

Burkholderia cepacia↗

PubMed2003

[Advances in safety studies of soil Bt toxin proteins released from transgenic Bt crops].

Commercialized transgenic Bt (Bacillus thuringiensis) crops are permitted for field growth in a large scale, which leads to significant issues of ecological risk assessment in soil ecosystem. In this paper, some general safety problems involving in the soil Bt active toxins released from insect-resistant transgenic Bt crops in the forms of plant residues, root exudates and pollens were reviewed, including their adsorption by soil active-particles, their insecticidal activity, persistence, and biodegradation by soil microbes, and their effects on soil organisms.

Bacterial Toxins↗

PubMed2003

[Effect of transgenic Bt rice planting on soil enzyme activities].

A pot experiment was conducted with silty loam Agrodolf as test soil and with transgenic Bt rice and non-Bt rice as test crops to study the effect of transgenic Bt rice planting on soil urease, phophatase, arylsulfatase, invertase, and dehydrogenase activities. The results showed that Bt toxin could be introduced into soil through root exudates of transgenic Bt rice, and its survival amount in soil varied with time. Compared with non-Bt rice treatment, transgenic Bt rice treatment had a significant decrease (2.47%) of soil urease activity and a significant increase (8.91%) of soil acid phosphatase activity, but no significant change in soil arylsulfatase, invertase, and dehydrogenase activities at the 15th day of emergence. At the 30th day of emergence, the transgenic Bt rice treatment still had a significant decrease of soil urease activity (16.36%) and a significant increase of acid phosphatase activity (35.69%), and no change in invertase activity. It also had significant increase in soil arylsulfatase (19.70%) and dehydrogenase activities (16.83%).

Bacillus thuringiensis Toxins↗