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PubMed1999

Comparison of bacterial community structures in the rhizoplane of tomato plants grown in soils suppressive and conducive towards bacterial wilt.

It has been reported that the growth of Ralstonia solanacearum is suppressed at the rhizoplane of tomato plants and that tomato bacterial wilt is suppressed in plants grown in a soil (Mutsumi) in Japan. To evaluate the biological factors contributing to the suppressiveness of the soil in three treated Mutsumi soils (chloroform fumigated soil; autoclaved soil mixed with intact Mutsumi soil; and autoclaved soil mixed with intact, wilt-conducive Yamadai soil) infested with R. solanacearum, we bioassayed soil samples for tomato bacterial wilt. Chloroform fumigation increased the extent of wilt disease. More of the tomato plant samples wilted when mixed with Yamadai soil than when mixed with Mutsumi soil. Consequently, the results indicate that the naturally existing population of microorganisms in Mutsumi soil was significantly able to reduce the severity of bacterial wilt of tomato plants. To characterize the types of bacteria present at the rhizoplane, we isolated rhizoplane bacteria and classified them into 22 groups by comparing their 16S restriction fragment length polymorphism patterns. In Yamadai soil a single group of bacteria was extremely predominant (73.1%), whereas in Mutsumi soil the distribution of the bacterial groups was much more even. The 16S rDNA sequence analysis of strains of dominant groups suggested that gram-negative bacteria close to the beta-proteobacteria were most common at the rhizoplane of the tomato plants. During in vitro assays, rhizoplane bacteria in Mutsumi soil grew more vigorously on pectin, one of the main root exudates of tomato, compared with those in Yamadai soil. Our results imply that it is difficult for the pathogen to dominate in a diversified rhizobacterial community that thrives on pectin.

Bacteria↗

PubMed2000

The stachydrine catabolism region in Sinorhizobium meliloti encodes a multi-enzyme complex similar to the xenobiotic degrading systems in other bacteria.

Stachydrine (proline betaine) can be used by Sinorhizobium meliloti as a source of carbon and nitrogen. Catabolism depends on an initial N-demethylation, after which the resultant N-methyl proline enters general metabolism. Deletion and insertion mutagenesis demonstrated that the information necessary for catabolism is carried on the symbiotic plasmid (pSym) distal to nodD2 and the nod-nif cluster. Sequencing of an 8.5kb fragment spanning this region revealed four open reading frames with functional homology to known proteins, including a putative monooxygenase and a putative NADPH-FMN-reductase, which were shown by insertional and frame-shift mutagenesis to be necessary for stachydrine catabolism. Other open reading frames, encoding a putative flavoprotein and a repressor, were judged not to be required for stachydrine catabolism, since they were not included in a fragment capable of complementing a deletion of the entire stc region. Sequence and mutagenesis data suggest that stachydrine is demethylated by an iron-sulfur monooxygenase of the Rieske type with a requirement for a specific reductase. The stc catabolic cluster, therefore, resembles xenobiotic degradation in other bacteria and recalls rhizopine catabolism in S. meliloti. Stachydrine appears to have multiple roles in osmoprotection, nutrition and nodulation. Genes involved in stachydrine catabolism are also necessary for carnitine degradation; thus, they could be important in the catabolism of a variety of root exudates and mediate other relationships.

Amino Acid Sequence↗

PubMed1993

A Rhizobium tropici DNA region carrying the amino-terminal half of a nodD gene and a nod-box-like sequence confers host-range extension.

Rhizobium tropici CIAT899 is a broad-host-range strain that, in addition to Phaseolus, nodulates other plant legumes such as Leucaena and Macroptilium. The narrow-host-range of Rhizobium leguminosarum biovars phaseoli (strain CE3) and trifolii (strain RS1051) can be extended to Leucaena esculenta and Phaseolus vulgaris plants, respectively, by the introduction of a DNA fragment 521 bp long, which carries 128 amino acids of the amino-terminal region of a nodD gene from R. tropici, as well as a putative nod-box-like sequence, divergently oriented. The 521 bp fragment, in the presence of L. esculenta or P. vulgaris root exudates, induced a R. leguminosarum bv. viciae nodA-lacZ fusion in either a CE3 or RS1051 background, respectively.

Amino Acid Sequence↗

PubMed2025

Sphingobium yanoikuyae 41R9 Enhances Nitrogen Uptake by Modulating Transporter Genes and Root Development in Rapeseed.

Plant growth-promoting rhizobacteria (PGPR) are widely recognized for enhancing the absorption of mineral nutrients by crops. While Sphingobium species have been reported as PGPRs, their capacity to improve nitrogen use efficiency (NUE) and the underlying regulatory mechanisms are not yet fully understood. Here, a strain 41R9, isolated from the rhizosphere of N-deficient rapeseed, was found to significantly enhance the growth performance of rapeseed under both low and normal N conditions. Genomic analysis revealed that strain 41R9 was closely related to Sphingobium yanoikuyae. 15N isotope tracer experiments confirmed that inoculation with strain 41R9 significantly boosted N uptake and translocation in rapeseed roots. Transcriptome profiling demonstrated that strain 41R9 directly upregulated N transporter genes (NRT2.5 and SLAH1/3), facilitating efficient N acquisition. Furthermore, strain 41R9 maintained jasmonic acid (JA) homoeostasis via JAZ-mediated negative feedback, balancing defense responses and root development, thereby improving the plant's N acquisition capacity in the roots. Metabolomic and in vitro assays further demonstrated that strain 41R9 displayed strong chemotaxis towards kaempferol, a N-deficiency-induced root exudate, suggesting kaempferol might as a chemical effector for S. yanoikuyae recruitment. These findings advance our understanding of PGPR-driven mechanisms in enhancing crop NUE and highlight the potential of harnessing PGPRs for sustainable agriculture.

Plant Roots↗

PubMed2001

Susceptibility to the sugar beet cyst nematode is modulated by ethylene signal transduction in Arabidopsis thaliana.

Previously, we identified Arabidopsis thaliana mutant rhd1-4 as hypersusceptible to the sugar beet cyst nematode Heterodera schachtii. We assessed rhd1-4 as well as two other rhd1 alleles and found that each exhibited, in addition to H. schachtii hypersusceptibility, decreased root length, increased root hair length and density, and deformation of the root epidermal cells compared with wild-type A. thaliana ecotype Columbia (Col-0). Treatment of rhd1-4 and Col-0 with the ethylene inhibitors 2-aminoethoxyvinylglycine and silver nitrate and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid suggests that the rhd1-4 hypersusceptibility and root morphology phenotypes are the result of an increased ethylene response. Assessment of known ethylene mutants further support the finding that ethylene plays a role in mediating A. thaliana susceptibility to H. schachtii because mutants that overproduce ethylene (eto1-1, eto2, and eto3) are hypersusceptible to H. schachtii and mutants that are ethylene-insensitive (etr1-1, ein2-1, ein3-1, eir1-1, and axr2) are less susceptible to H. schachtii. Because the ethylene mutants tested show altered susceptibility and altered root hair density and length, a discrimination between the effects of altered ethylene signal transduction and root hair density on susceptibility was accomplished by analyzing the ttg and gl2 mutants, which produce ectopic root hairs that result in greatly increased root hair densities while maintaining normal ethylene signal transduction. The observed normal susceptibilities to H. schachtii of ttg and g12 indicate that increased root hair density, per se, does not cause hypersusceptibility. Furthermore, the results of nematode attraction assays suggest that the hypersusceptibility of rhd1-4 and the ethylene-overproducing mutant eto3 may be the result of increased attraction of H. schachtii-infective juveniles to root exudates of these plants. Our findings indicate that rhd1 is altered in its ethylene response and that ethylene signal transduction positively influences plant susceptibility to cyst nematodes.

Amino Acids, Cyclic↗

PubMed2000

Rhizosphere Interactions and the Exploitation of Microbial Agents for the Biological Control of Plant-Parasitic Nematodes.

A range of specialist and generalist microorganisms in the rhizosphere attacks plant-parasitic nematodes. Plants have a profound effect on the impact of this microflora on the regulation of nematode populations by influencing both the dynamics of the nematode host and the structure and dynamics of the community of antagonists and parasites in the rhizosphere. In general, those organisms that have a saprophytic phase in their life cycle are most affected by environmental conditions in the rhizosphere, but effects on obligate parasites have also been recorded. Although nematodes influence the colonization of roots by pathogenic and beneficial microorganisms, little is known of such interactions with the natural enemies of nematodes in the rhizosphere. As nematodes influence the quantity and quality of root exudates, they are likely to affect the physiology of those microorganisms in the rhizosphere; such changes may be used as signals for nematode antagonists and parasites. Successful biological control strategies will depend on a thorough understanding of these interactions at the population, organismal, and molecular scale.

cyst nematodes↗

PubMed2006

Studying plant-microbe interactions using stable isotope technologies.

Interactions between plants and microorganisms in the rhizosphere are complex and varied. They include the general transfer of nutrients and specific interactions mediated by the release of signalling molecules from plant roots. Until recently, understanding the nature of these interactions was limited by a reliance on traditional, cultivation-based techniques. Stable isotope probing provides the potential for cultivation-independent characterisation of organisms actively assimilating carbon derived from plant root exudate or added to the soil. Current applications have focused on interactions with relatively low-level specificity, but there is significant potential for mechanistic studies of more specific interactions, particularly if the sensitivity of the technique can be increased.

Bacteria↗

PubMed2006

[Research advances in phytoremediation of polychiorinated biphenyls (PCBS)].

This paper reviewed the research advance in PCBs phytoremediation, with the focus on the roles and mechanisms of plants in the removal of PCBs from the environment. In the process of PCBs removal, plants acted not only as a supporter of biodegradation, but also as an active participator in metabolism. Plants could absorb and accumulate PCBs from the environment, and store the non-toxic metabolic products in their tissues. Root exudates could degrade PCBs directly by the contained ectoenzymes, or indirectly through stimulating the activity of rhizospheric microbes. The internal and external factors affecting the phytoremediation of PCBs, including plant species, their culture types and biomass, as well as the initial concentration of PCBs and their physical and chemical characters, were also discussed.

Biodegradation, Environmental↗

PubMed2001

FUNCTION AND MECHANISM OF ORGANIC ANION EXUDATION FROM PLANT ROOTS.

The rhizosphere is the zone of soil immediately surrounding plant roots that is modified by root activity. In this critical zone, plants perceive and respond to their environment. As a consequence of normal growth and development, a large range of organic and inorganic substances are exchanged between the root and soil, which inevitably leads to changes in the biochemical and physical properties of the rhizosphere. Plants also modify their rhizosphere in response to certain environmental signals and stresses. Organic anions are commonly detected in this region, and their exudation from plant roots has now been associated with nutrient deficiencies and inorganic ion stresses. This review summarizes recent developments in the understanding of the function, mechanism, and regulation of organic anion exudation from roots. The benefits that plants derive from the presence of organic anions in the rhizosphere are described and the potential for biotechnology to increase organic anion exudation is highlighted.

Journal Article↗

PubMed2005

Microbial activity related to N cycling in the rhizosphere of maize stressed by heavy metals.

A greenhouse experiment was carried out to compare differences in potential activities of ammonification, nitrification and denitrification in rhizosphere and bulk soil in a heavy-metal-stressed system. Exchangeable fractions of Cd, Cu and Cr were all higher in the rhizosphere of maize than in bulk soil. Results showed that the mineralization of N in soil was stimulated by low concentration of Cd. Addition of Cd at low levels stimulated the ammonifying and nitrifying activity in soil, while inhibitory influences were shown at high levels. Nitrifying bacteria was proved to be the most sensitive one, whilst the effect on denitrifying bacteria was very limited. Comparing Cd, Cu and Cr(VI) at 20 mg/kg soil, Cd was the most effective inhibitor of ammonification and denitrification, while Cr(VI) had the strongest inhibitory influence on nitrifying activity. Root exudates played important roles on the different exchangeable metal fractions and bacterial activities between rhizosphere and non-rhizosphere. Nitrate was the main form of mineral N in soil, as well as the main form of N absorbed by plants, but the formation and relative absorption of ammonium were promoted in response to high Cd exposure.

Bacteria↗

PubMed2004

The allelochemical sorgoleone inhibits root H+-ATPase and water uptake.

Sorghum plants inhibit the growth of some adjacent species. Root exudates from grain sorghum (Sorghum bicolor), consisting primarily of the quinone sorgoleone, are phytotoxic to several plant species, yet the mechanisms of growth inhibition remain to be fully explained. Disruption of electron transport functions in isolated mitochondria and chloroplasts has been reported as one explanation for growth inhibition. In the studies reported here, however, soybean seedlings grown in nutrient solution with 10, 50, or 100 microM sorgoleone showed no disruption of photosynthesis, as measured by leaf fluorescence and oxygen evolution, yet their mean leaf surface area was less when grown in 100 microM sorgoleone. Furthermore, in the presence of these same concentrations of sorgoleone, decreased nutrient solution use by soybean seedlings and decreased H+-ATPase activity in corn root microsomal membranes were observed. This suggests that impairment of essential plant processes, such as solute and water uptake, driven by proton-pumping across the root cell plasmalemma should also be considered as a mechanism contributing to observed plant growth inhibition by sorgoleone.

Benzoquinones↗

PubMed1981

Control of microorganisms in the rhizosphere of wheat by inoculation of seeds with Pseudomonas putida and by foliar application of urea.

After inoculation of wheat seeds with various bacterial strains germination of plants was usually inhibited at first but growth was stimulated later. After inoculation with Pseudomonas putida K 11 producing physiologically active compounds the total number of bacteria increased together with the bacteria: fungi ratio in the rhizosphere. These characteristic were further increased after foliar application of urea due to increased root exudation. Dry mass of upper wheat parts was about 14--80% higher in green-house experiments, in which the plants were treated in the two above ways. More reliable results were usually obtained by bacterization of P. putida and foliar application of urea as compared with the situation when the seeds were inoculated without the foliar application or, on the contrary, after foliar application without inoculation of the seeds. Only when urea was applied early and ain a soil contaminated with the fungus Gaeumannomyces graminis var. tritici (causing "take-all" of the wheat) no favourable results could be detected. In these cases the foliar application without inoculation of the seeds was more successful. Symptoms of the disease of wheat roots caused by G. graminis were less frequently observed after the inoculation of the seeds with the strain P. putida K 11 and after the foliar application of urea.

Ecology↗

PubMed2006

Functional characterization of desaturases involved in the formation of the terminal double bond of an unusual 16:3Delta(9,12,150) fatty acid isolated from Sorghum bicolor root hairs.

Sorgoleone, produced in root hair cells of sorghum (Sorghum bicolor), is likely responsible for much of the allelopathic properties of sorghum root exudates against broadleaf and grass weeds. Previous studies suggest that the biosynthetic pathway of this compound initiates with the synthesis of an unusual 16:3 fatty acid possessing a terminal double bond. The corresponding fatty acyl-CoA serves as a starter unit for polyketide synthases, resulting in the formation of 5-pentadecatrienyl resorcinol. This resorcinolic intermediate is then methylated by an S-adenosylmethionine-dependent O-methyltransferase and subsequently dihydroxylated, yielding the reduced (hydroquinone) form of sorgoleone. To characterize the corresponding enzymes responsible for the biosynthesis of the 16:3 fatty acyl-CoA precursor, we identified and cloned three putative fatty acid desaturases, designated SbDES1, SbDES2, and SbDES3, from an expressed sequence tag (EST) data base prepared from isolated root hairs. Quantitative real-time RT-PCR analyses revealed that these three genes were preferentially expressed in sorghum root hairs where the 16:2 and 16:3 fatty acids were exclusively localized. Heterologous expression of the cDNAs in Saccharomyces cerevisiae revealed that recombinant SbDES2 converted palmitoleic acid (16:1Delta(9)) to hexadecadienoic acid (16:2Delta(9,12)), and that recombinant SbDES3 was capable of converting hexadecadienoic acid into hexadecatrienoic acid (16:3Delta(9,12,15)). Unlike other desaturases reported to date, the double bond introduced by SbDES3 occurred between carbons 15 and 16 resulting in a terminal double bond aliphatic chain. Collectively, the present results strongly suggest that these fatty acid desaturases represent key enzymes involved in the biosynthesis of the allelochemical sorgoleone.

Amino Acid Sequence↗

PubMed2005

In situ stable isotope probing of methanogenic archaea in the rice rhizosphere.

Microorganisms living in anoxic rice soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of rice plants with 13CO2 resulted in incorporation of 13C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.

Archaea↗

PubMed2004

A novel laboratory screening bioassay for crop seedling allelopathy.

Crops that control weeds by root exudation of allelochemicals are receiving increased attention, and there are efforts to breed allelopathic cultivars in several crops. The genetic improvement of allelopathic traits is based upon parental germ plasm with high allelopathic activity. Identification of allelopathic germplasm is done in laboratory screening bioassays, but experimental protocols are limited. We developed a fast and reliable laboratory screening bioassay for grain crops that includes dose-response considerations as an integral part of the experimental design. The bioassay was conducted in hydroponic culture, and a range of experiments with 2-(3H)-benzoxazolinone (BOA), an allelochemical of several grain crops, was carried out to define the basic protocol. Because of its sensitivity to BOA, Sinapis alba L. was selected as the receiver species. BOA affected growth (fresh weight and length of shoot and root), enzyme activities (ascorbate peroxidase, catalase, glutathione S-transferase, peroxidase, phenylalanine ammonia-lyase), and chlorophyll fluorescence, whereby root length was the most reliable response parameter. BOA sensitivity was dependent on nutrients for all parameters measured, and, thus, no nutrients were added. A set of experiments with Secale cereale L. and Triticum aestivum L. as donor species was carried out to optimize the protocol. Light and pH were eliminated as primary causes for the observed inhibition. The proposed bioassay has several methodological advantages over current bioassays.

Benzoxazoles↗

PubMed2005

The mycorrhizal fungus Gigaspora margarita possesses a CuZn superoxide dismutase that is up-regulated during symbiosis with legume hosts.

A full-length cDNA showing high similarity to previously described CuZn superoxide dismutases (SODs) was identified in an expressed sequence tag collection from germinated spores of the arbuscular mycorrhizal fungus Gigaspora margarita (BEG 34). The corresponding gene sequence, named GmarCuZnSOD, is composed of four exons. As revealed by heterologous complementation assays in a yeast mutant, GmarCuZnSOD encodes a functional polypeptide able to confer increased tolerance to oxidative stress. The GmarCuZnSOD RNA was differentially expressed during the fungal life cycle; highest transcript levels were found in fungal structures inside the roots as observed on two host plants, Lotus japonicus and Medicago truncatula. These structures also reacted positively to 3,3'-diaminobenzidine, used to localize H2O2 accumulation. This H2O2 is likely to be produced by CuZnSOD activity since treatment with a chelator of copper ions, generally used to inhibit CuZnSODs, strongly reduced the 3,3'-diaminobenzidine deposits. A slight induction of GmarCuZnSOD gene expression was also observed in germinated spores exposed to L. japonicus root exudates, although the response showed variation in independent samples. These results provide evidence of the occurrence, in an arbuscular mycorrhizal fungus, of a functional SOD gene that is modulated during the life cycle and may offer protection as a reactive oxygen species-inactivating system against localized host defense responses raised in arbuscule-containing cells.

Amino Acid Sequence↗

PubMedDate not supplied

[Study of chemotaxis of nodule bacteria of lupin to organic substances].

Ability of different strains (359a, 400, 176, 365a) of nodule bacteria of lupin Bradyrhizobium sp. (Lupinus), which differ in symbiotic properties (competitiveness and nitrogen-fixing activity), to chemotaxis with respect to the organic substances revealed in root exudates of lupin (aminoacids, sugars, organic acids and their salts) has been investigated. It is shown, that alongside with the substances to which rhizobia of lupin, irrespective of their symbiotic properties, show the chemotaxic reactions, there is a number of substances which are specific with respect to different strains of bacteria. Selectivity in chemotaxis of the nodule bacteria depends on their competitiveness. The relations between nitrogen-fixing activity of strains and their ability to chemotaxis are not established.

Acids↗

PubMed2005

Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal (AM) fungi form mutualistic, symbiotic associations with the roots of more than 80% of land plants. The fungi are incapable of completing their life cycle in the absence of a host root. Their spores can germinate and grow in the absence of a host, but their hyphal growth is very limited. Little is known about the molecular mechanisms that govern signalling and recognition between AM fungi and their host plants. In one of the first stages of host recognition, the hyphae of AM fungi show extensive branching in the vicinity of host roots before formation of the appressorium, the structure used to penetrate the plant root. Host roots are known to release signalling molecules that trigger hyphal branching, but these branching factors have not been isolated. Here we have isolated a branching factor from the root exudates of Lotus japonicus and used spectroscopic analysis and chemical synthesis to identify it as a strigolactone, 5-deoxy-strigol. Strigolactones are a group of sesquiterpene lactones, previously isolated as seed-germination stimulants for the parasitic weeds Striga and Orobanche. The natural strigolactones 5-deoxy-strigol, sorgolactone and strigol, and a synthetic analogue, GR24, induced extensive hyphal branching in germinating spores of the AM fungus Gigaspora margarita at very low concentrations.

Chromatography, High Pressure Liquid↗