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PubMed1988

Identification of nodX, a gene that allows Rhizobium leguminosarum biovar viciae strain TOM to nodulate Afghanistan peas.

Gene(s) conferring the ability of Rhizobium leguminosarum biovar viciae strain TOM to nodulate primitive peas (cultivar Afghanistan) had been located in a 2.0 kb region of its sym plasmid, pRL5JI. In this DNA, a single open reading frame of 1101 bp, corresponding to a gene, nodX was found. nodX is downstream of nodJ which is present in strain TOM and also in the sym plasmid of a typical strain of this biovar. nodX specifies a hydrophobic protein (of Mr 41,036) with no clear similarity to other proteins in data bases. Mutations in nodX abolished nodulation of Afghanistan peas but not nodulation of commercial peas. nodX-lacZ fusions were used to show that transcription of nodX was activated by root exudates from both commercial and Afghanistan peas and by defined flavonoids. Exudate from Afghanistan peas activated nod genes of typical strains of R. leguminosarum biovar viciae which fail to nodulate these peas; thus, their failure to nodulate these primitive peas is not due to a lack of activation of their nod genes by exudate from Afghanistan peas. A homologue of nodX exists in R. leguminosarum biovar trifolii (which nodulates clover) but not in typical strains of R. leguminosarum biovar viciae.

Base Sequence↗

PubMed1984

Effect of soil fungistasis on zoopathogenic fungi.

The inhibiting action of west-Siberian soils on spore germination and the growth and development of zoopathogenic fungi such as Emmonsia (Chrysosporium) crescens , Trichophyton mentagrophytes, Beauveria bassiana , Metarrhizium anisopliae , Paecilomyces farinosus , P. fumoso -roseus and Chrysosporium keratinophilum have been studied by the authors. The influence of carbon sources and the root exudates of plants on fungistasis have also been studied.

Carbohydrate Metabolism↗

PubMed1998

Localization of nod, nif, and acidic exopolysaccharide determinants on a large plasmid in slow-growing cowpea Rhizobium sp. S2.

Slow-growing cowpea Rhizobium sp. S2, a pigeon pea isolate, showed excessive synthesis of exopolysaccharide (EPS) and nod factor(s) only when grown in the presence of corresponding host root exudate (RE) or naringenin (a flavonoid present in RE of pigeon pea). muc- strain, a plasmid-cured derivative of the parent strain, showed negligible EPS production and failed to synthesize the nod factor(s) under similar growth conditions. The nod factor(s) was extracted and partially purified from the total EPS of the culture supernatant of S2 grown in the presence of either RE or naringenin by the butanol-soluble, ethyl acetate-insoluble method. The parent strain also showed ex-planta nitrogenase activity, whereas in muc- it was not detectable. In contrast to observations of the location of nod, nif- and EPS-synthesizing genes on the chromosome in commonly studied cowpea Rhizobia and Bradyrhizobium sp. colony blot and dot blot hybridization studies revealed the presence of nod (common nod genes), nif (nif KDH); and EPS (pss) determinants to be on the large plasmid in the parent strain and therefore absent in muc-, which is a plasmid-cured derivative.

Genes, Bacterial↗

PubMed2005

Transgenic expression of a novel M. truncatula phytase gene results in improved acquisition of organic phosphorus by Arabidopsis.

A full-length cDNA encoding an extracellular form of phytase was isolated from the model legume Medicago truncatula. The phytase cDNA (MtPHY1) has an open reading frame of 1,632 bp predicted to encode 543 amino acids including an N-terminal signal peptide of 27 amino acids. The MtPHY1 gene is 5,151 bp in length, containing 7 exons and 6 introns. MtPHY1 transcripts were detected in leaves and roots and levels elevated in roots during growth in low phosphate conditions. Transgenic Arabidopsis lines expressing MtPHY1 under the control of the root-specific MtPT1 promoter or the constitutive CaMV35S promoter were created. Phytase activities in root apoplast of the transgenic Arabidopsis were 12.3- to 16.2-fold higher than those of the control plants. The expressed phytase was secreted into the rhizosphere as demonstrated by enzyme activity staining and HPLC analysis of phytate degradation by root exudates. Transgenic expression of the MtPHY1 led to significant improvement in organic phosphorus utilization and plant growth. When phytate was supplied as the sole source of phosphorus, dry weight of the transgenic Arabidopsis lines were 3.1- to 4.0-fold higher than the control plants and total phosphorus contents were 4.1- to 5.5-fold higher than the control. Transgenic expression of phytase genes of plant origin has great potential for improving plant phosphorus acquisition and for phytoremediation.

6-Phytase↗

PubMed2026

Microbial partnerships and molecular mechanisms in plant stress physiology for climate-resilient and sustainable farming.

Plant-microbial partnerships and their underlying molecular mechanisms are indispensable, natural drivers of improved nutrient acquisition and stress tolerance in the face of climate-driven environmental challenges. Modern multi-omics tools, when coupled with artificial intelligence and synthetic biology, enable the precise design of targeted bioinoculants and synthetic microbial consortia. Translating these advanced microbiome-based strategies into scalable, field-level agricultural applications provides a sustainable path toward securing global food production while maintaining soil health. Global climate change imposes multifaceted abiotic and biotic stresses on crops, disrupting physiological and molecular processes and threatening agricultural productivity. Plant-associated microbes represent an underexplored yet powerful ally in enhancing crop resilience. This review presents current knowledge of plant-microbe interactions and the molecular mechanisms governing plant stress physiology, with an emphasis on climate-resilient and sustainable farming. Hence, ever-changing environmental cues pose a significant burden on agricultural productivity, and plant-associated microbial communities modulate a cascade of physiological and molecular responses, including production of phytohormones, signaling, regulation of reactive oxygen species homeostasis, and activation of plant immune responses to help plants withstand stress and enhance productivity. Moreover, root exudates, phytohormones, and quorum sensing mediate the central communication networks, facilitating plant-microbe cross talk. Additionally, the advances in OMICs approaches aid in disentangling the molecular underpinnings of these interactions by providing mechanistic insights and potential candidate gene targets for crop improvement and stress resilience. In the post-genomic era, integrating artificial intelligence and big data analysis to optimize microbiome-based strategies for sustainable agriculture is a new frontier for disentangling plant-microbe symbiosis to improve soil health, enhance crop yields, and improve stress tolerance. Thus, by integrating the ecological, physiological, and molecular perspectives, this review highlights the transformative potential of harnessing plant-microbe symbiosis for climate-resilient and sustainable agriculture.

Stress, Physiological↗

PubMed2002

Identification of mono-, oligo-, and polysaccharides secreted from soybean roots.

The mist culture system was conducted to study secreted polysaccharides from soybean ( Glycine max) roots grown for 15 days. Roots were rinsed with distilled water (DW) for 15 min, then with 30 mM oxalic acid (OXA) for 15 min to remove ionically bound sugar. Released sugars were further fractionated into low (L) and high (H) molecular weight fractions with Sephadex G-10. DW rinsing released 190 microg neutral sugar (NS) and 62 microg uronic acid (UA) per plant, while 374 microg NS and 70 microg UA per plant were released by OXA rinsing. Acetylation analysis revealed that the L fraction by DW and OXA mainly consisted of glucose (Glc), pinitol, and UA, whereas the H fraction mainly consisted of arabinose (Ara), galactose (Gal), Glc, and UA. The presence of rhamnose (2%-6%) in both fractions suggests secretion of rhamnogalacturonans. Methylation analysis revealed that the H fraction by DW and OXA contained T-Ara, 3-, 6-, and 3,6-Gal, suggesting the presence of type II arabinogalactan and arabinogalactan proteins. HPLC analysis detected mono-, di-, and tri-GalA in the L fraction by DW and OXA. Substances corresponding to sucrose, kojibiose, cello- and laminari-oligosaccharides were also found in root exudates.

Journal Article↗

PubMed1995

Studies on uptake of trivalent and hexavalent chromium by maize (Zea mays).

Pot culture experiments were carried out to study the uptake and translocation of chromium from irrigation water when supplied in its trivalent and hexavalent states to maize plants grown in soil and sand culture. The uptake of chromium was observed to increase with increase in the concentration for both oxidation states of chromium. For the root, the observed order of uptake was CrIII sand > CrVI sand > CrIII soil > CrVI soil, whereas in the lower shoot, upper shoot and fruit the order was CrVI sand > CrVI soil > CrIII sand > CrIII soil. Significantly high uptake of chromium by roots in the sand culture (CrIII treatment) is attributed to the effect of root exudates and degradation products on the mobilization of CrIII. In aerial parts of the plants a higher uptake was observed when the initial supply was CrVI. The trends observed are explained on the basis of the redox behaviour of chromium.

Chromium↗

PubMed2005

Degradability of dissolved soil organic carbon and nitrogen in relation to tree species.

The degradability and chemical characteristics of water-extractable dissolved organic carbon (DOC) and nitrogen (DON) from the humus layer of silver birch (Betula pendula Roth), Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.) stands were compared in short-term incubation of soil solutions. For all extracts the degradation of DOC and DON was low (12-17% loss) and increased in the order: birch, spruce and pine. In the humus layer under pine a relatively larger pool of rapidly degrading dissolved soil organic matter (DOM) was indicated by the [3H]thymidine incorporation technique, which measures the availability of DOM to bacteria. The degradation of DOC was explained by a decrease in the hydrophilic fraction. For DON, however, both the hydrophilic and hydrophobic fractions tended to decrease during incubation. No major differences in concentrations of hydrophilic and hydrophobic fractions were detected between tree species. Molecular size distribution of DOC and DON, however, revealed slight initial differences between birch and conifers as well as a change in birch extract during incubation. The depletion of very rapidly degrading fractions (e.g., root exudates and compounds from the litter) may explain the low degradability of DOM in the humus layer under birch.

Analysis of Variance↗

PubMed2026

Strigolactones constrain rice drought acclimation by suppressing ROS scavenging through the D53-OsWRKY31-ZFP36 module.

Strigolactones (SLs) are a class of plant hormones essential for tiller development and yield under diverse environmental conditions. Drought is a major limiting factor for rice yields. Although SLs contribute to drought resistance, mechanisms and practical applications of SL pathway in drought acclimation of rice remain poorly understood. Our study shows that short-term dehydration represses SL biosynthesis in rice roots. Genetic assays indicate that disruption of SL biosynthesis or signaling elevates rice drought resistance, whereas SL signaling activation or supplementation with the SL analog GR244DO impairs drought resistance. SLs negatively regulate drought acclimation by promoting degradation of the repressor protein DWARF53 (D53). D53 interacts with the transcription factor OsWRKY31 via its N-terminal domain and suppresses the protein level of OsWRKY31, which binds to and represses transcription of the ZFP36 promoter. ZFP36 encodes a zinc-finger transcription factor that promotes H2O2 scavenging to sustain reactive oxygen species (ROS) homeostasis during drought stress. Notably, the drought-resistant upland rice variety IRAT109 exhibits lower SL levels in root exudates than the lowland rice variety Nipponbare (NP). Genome editing of key components in SL pathway enhances drought resistance in NP, Huazhan (HZ), and IRAT109. The agronomic potential of tuning SL biosynthesis is further supported by the elite D17/HTD1 allele, which weakens SL biosynthesis and improves drought resistance and grain yield in Nekken 2 (NK2) under field conditions. These findings uncover a key mechanism underlying SL-repressed drought acclimation in rice and provide an effective strategy to improve drought resistance in diverse rice varieties amid ongoing climate change.

D53↗

PubMed2006

Labile substrates quality as the main driving force of microbial mineralization activity in a poplar plantation soil under elevated CO2 and nitrogen fertilization.

Soil carbon (C) long term storage is influenced by the balance among ecosystem net primary productivity (NPP), the rate of delivery of new organic matter to soil pools and the decomposition of soil organic matter (SOM). The increase of NPP under elevated CO(2) can result in a greater production and higher turnover of fine roots or root exudation and, in turn, in an increase of labile C belowground. The aim of this work was to detect if changes in labile C substrates influenced the organic C storage in soils, verifying (i) whether treatments with elevated CO(2) and N fertilization induced changes in the amount and quality of labile C pools and in microbial C immobilization and (ii) whether these changes provoked modifications in the microbial C mineralization activity, and therefore changes in soil C losses. The effect of elevated CO(2) was a significant increase in both seasons (June and October 2004), of all labile C fractions: microbial biomass C (MBC), K(2)SO(4) extractable C (ExC), and water soluble C (WSC). The C/N ratio of the microbial biomass and of the K(2)SO(4) extractable SOM presented a seasonal fluctuation showing higher values in June, whereas the elevated CO(2) increased significantly the C/N ratio of these fractions independent of the season and the N addition, indicating a lower quality of labile SOM. Microbial respiration was more than doubled in October compared to June, confirming that changes in substrate quality and nutrient availability, occurring in the plantation at the beginning and at the end of the vegetative period, influenced the microbial activity in the bulk soil. Furthermore, the microbial respiration response to N fertilization was dependent on the season, with an opposite effect between June and October. The kinetic parameters calculated according to the first-order equation C(m)=C(0)(1-e(-kt)) were unaffected by elevated CO(2) treatment, except C(0)k and MR(basal), that showed a significant reduction, ascribable to (i) a lower quality of labile pools, and (ii) a more efficient microbial biomass in the use of available substrates. The C surplus found in elevated CO(2) soils was indeed immobilized and used for microbial growth, thus excluding a priming effect mechanism of elevated CO(2) on SOM decomposition.

Carbon↗

PubMed2001

Exploring correlation between redox potential and other edaphic factors in field and laboratory conditions in relation to methane efflux.

Methane is primarily a biogenic gas, which is implicated in global warming. Although its production in the anoxic conditions is regulated by several edaphic factors, aquatic macrophytes also influence methane emission by providing aerenchyma to act as chimney for CH4 transport from the sediment to troposphere, by releasing root exudates to the sediment to serve as substrate for methanogenic bacteria and by transporting atmospheric O2 to rhizosphere, which stimulates CH4 consumption. Among the edaphic factors, redox potential (Eh) is the most important, which largely determines the action of methanogenic bacteria. Hence, a study was undertaken first to find out the correlation between CH4 emission and edaphic factors in the field conditions and then to understand the relationship between Eh and other edaphic factors. The field studies revealed that natural wetlands were the major source of CH4 emission, and the vegetation plays an important role in CH4 emission from the water bodies. However, it was very difficult to establish a strong relationship between the CH4 emission and the edaphic factors in the field conditions due to other limiting factors and their constant fluctuations. In this connection, the laboratory experiments exhibited that soil temperature, pH, moisture regime and incubation period were negatively correlated with Eh, which determines the initiation of methanogenic process. However, organic carbon and the water regime over the soil surface did not show any impact on Eh in this study.

Air Pollutants↗

PubMed2003

[Potential role of winter rape weeds in the extension of broomrape in Poitou-Charentes].

In the Poitou-Charentes district, among the 82 species of winter rape weeds identified, 22 displayed a strong affinity for this crop (Brassica napus L.). In fields, 50% of these weeds were parasitized by Orobanche ramosa, playing the role of host plants. Greenhouse co-cultures (weed/Orobanche ramosa) showed that weeds non-parasitized in fields could be attacked by broomrape, developing a more or less complete cycle. In vitro co-cultures (weed/Orobanche ramosa) revealed that root exudates of non-parasitized weeds, in fields or in greenhouse co-cultures, could induce Orobanche ramosa seed germination, but not attachment. These weeds could play the role of false hosts.

Brassica napus↗

PubMed1998

A new photosystem II electron transfer inhibitor from Sorghum bicolor.

Our study of the mechanism(s) by which sorgoleone (1) acts as a photosystem II (PS II) inhibitor led to the isolation of a new benzoquinone derivative, 2-hydroxy-5-ethoxy-3-[(Z,Z)-8',11', 14'-pentadecatriene]-rho-benzoquinone (2), from the root exudate of sorghum. The structure of 2, which is being given the name 5-ethoxy-sorgoleone, was determined by spectroscopic means. A methoxy derivative (3) of 1 was also prepared. Both 2 and 3 caused a reduction in oxygen evolution by thylakoid membranes and induced variable chlorophyll fluorescence. These compounds, however, were less active inhibitors of PS II than 1.

Benzoquinones↗

PubMed2000

Evolution of nitrogen fixation in spatially structured populations of Rhizobium.

Symbiosis between legumes and nitrogen-fixing bacteria is thought to bring mutual benefit to each participant. However, it is not known how rhizobia benefit from nodulation of legume hosts because they fix nitrogen only after differentiating into bacteroids, terminally differentiated cells that cannot reproduce. Because free-living rhizobia can reproduce, and may benefit from the increase of plant root exudates stimulated by nodulation, evolution of symbiotic nitrogen fixation may depend upon kin selection. However, unrelated nonmutualists may also benefit from increased plant exudates and nitrogen-fixing populations are therefore vulnerable to invasion by nonfixing, saprophytic Rhizobium. The access of nonfixing Rhizobium to the plant exudates associated with nodules depends upon the spatial structure of the Rhizobium populations within the soil. We investigate the influence of spatial structure on the evolution of N-fixation within a Rhizobium population using a mathematical model. Our model demonstrates that spatial structure is necessary for the evolution of N-fixation and that N-fixation is more likely to evolve with increasing degrees of spatial structure. In fact, we identify three dynamic outcomes that depend upon the relative strength of the costs of N-fixation relative to the degree of spatial structure and benefits resulting from nodulations. If the costs are relatively high, N-fixation will not evolve; if the costs are relatively low, N-fixing genes will fix in the population, but at intermediate conditions, a stable mixture of N-fixing bacteria and nonfixing bacteria will be maintained. The conditions for coexistence of N-fixing bacteria and nonfixing bacteria expand under a saturating relationship between nodule numbers and N-fixing genotype frequency.

Biological Evolution↗

PubMed2003

Host plant-dependent phenotypic reversion of Ralstonia solanacearum from non-pathogenic to pathogenic forms via alterations in the phcA gene.

Ralstonia solanacearum is a plant pathogenic bacterium that undergoes a spontaneous phenotypic conversion (PC) from a wild-type pathogenic to a non-pathogenic form. PC is often associated with mutations in phcA, which is a key virulence regulatory gene. Until now, reversion to the wild-type pathogenic form has not been observed for PC variants and the biological significance of PC has been questioned. In this study, we characterized various alterations in phcA (eight IS element insertions, three tandem duplications, seven deletions and a base substitution) in 19 PC mutants from the model strain GMI1000. In five of these variants, reversion to the pathogenic form was observed in planta, while no reversion was ever noticed in vitro whatever culture media used. However, reversion was observed for a 64 bp tandem duplication in vitro in the presence of tomato root exudate. This is the first report showing a complete cycle of phenotypic conversion/reversion in a plant pathogenic bacterium.

Bacterial Proteins↗

PubMed1982

Cytoplasmic male sterility in barley: Evidence for the involvement of cytokinins in fertility restoration.

The hypothesis of the association between an increase in cytokinin activity and restoration of anther fertility in msm1 cytoplasm was tested. The following barley lines with Hordeum vulgare cv. Adorra nuclear gene background were studied: Adorra cytoplasm without nuclear restorer gene (fertile), Adorra cytoplasm homozygous for nuclear Rfm1a gene (fertile), msm1 cytoplasm without restorer gene (male sterile), msm1 cytoplasm homozygous for nuclear Rfm1a gene (fertile). Ethanolic extracts of root exudate were fractionated and bioassayed for cytokinins. Both the biological activity and the total quantity of cytokinins appeared lowest in the unrestored male sterile line. The total biological activities of cytokinins in the three fertile lines were similar, but the quantities in the restorer gene carriers appeared lower. On the other hand, the restorer gene carriers, independent of the cytoplasm, showed 8-9 times more of a bound cytokinin. Because the bound form is evidently underestimated by the bioassay, the increase in the bound cytokinin fraction may mean even a higher total content in the Rfm1a gene carriers than in Adorra without the gene. The bound cytokinin may be translocated more readily to distal organs (e.g., the anthers) compared with unbound cytokinins. Because cytokinins are associated with various ecophysiological processes, the rise in a particular form may explain the heterogeneous distribution of the restorer gene in wild barley populations in different regions of Israel.

Journal Article↗

PubMed2003

The role of microbial reductive dechlorination of TCE at a phytoremediation site.

In April 1996, a phytoremediation field demonstration site at the Naval Air Station, Fort Worth, Texas, was developed to remediate shallow oxic ground water (< 3.7 m deep) contaminated with chlorinated ethenes. Microbial populations were sampled in February and June 1998. The populations under the newly planted cottonwood trees had not yet matured to an anaerobic community that could dechlorinate trichloroethene (TCE) to cis-1,2-dichloroethene (DCE); however, the microbial population under a mature (approximately 22-year-old) cottonwood tree about 30 m southwest of the plantings had a mature anaerobic population capable of dechlorinating TCE to DCE, and DCE to vinyl chloride (VC). Oxygen-free sediment incubations with contaminated groundwater also demonstrated that resident microorganisms were capable of the dechlorination of TCE to DCE. This suggests that a sufficient amount of organic material is present for microbial dechlorination in aquifer microniches where dissolved O2 concentrations are low. Phenol, benzoic acid, acetic acid, and a cyclic hydrocarbon, compounds consistent with the degradation of root exudates and complex aromatic compounds, were identified by gas chromatography/mass spectrometry (GC/MS) in sediment samples under the mature cottonwood tree. Elsewhere at the site, transpiration and degradation by the cottonwood trees appears to be responsible for loss of chlorinated ethenes.

Bacteria↗

PubMed2002

Symbiotic conditions induce structural modifications of Sinorhizobium sp. NGR234 surface polysaccharides.

When the rhizosphere is starved of nitrogen, the soil bacteria Rhizobium are able to infect legume roots and invade root nodules, where they can fix atmospheric nitrogen. Nod boxes, the nod gene promoters located on the rhizobial symbiotic plasmid, are activated by means of flavonoids present in the legume root exudates, leading to the synthesis of lipochitooligomers: the Nod factors. Several recent works pointed out the importance of rhizobial surface polysaccharides in establishing the highly specific symbiosis between rhizobia and legumes. Lipopolysaccharides (LPSs) exhibit specific active roles in the later stages of the nodulation processes, such as the penetration of the infection thread into the cortical cells or the setting up of the nitrogen-fixing phenotype. The study reported here concerns the structural modifications affecting surface (lipo)polysaccharides when Sinorhizobium sp. NGR234 strains are grown with nod gene induction under nitrogen starvation. In the absence of induction, NGR234 only produces fast-migrating LPSs. When cultured in the presence of flavonoids, the same strain produces large quantities of a high-molecular-weight rhamnose-rich lipopolysaccharide (RLPS). Because the synthesis of this compound seems to be coded by the symbiotic plasmid under direct or indirect gene induction by flavonoids, this RLPS is thought to be biologically relevant.

Bacterial Proteins↗