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PubMed1978

Biological dinitrogen fixation (acetylene reduction) associated with Florida mangroves.

Biological dinitrogen fixation in mangrove communities of the Tampa Bay region of South Florida was investigated using the acetylene reduction technique. Low rates of acetylene reduction (0.01 to 1.84 nmol of C(2)H(4)/g [wet weight] per h) were associated with plant-free sediments, while plant-associated sediments gave rise to slightly higher rates. Activity in sediments increased greatly upon the addition of various carbon sources, indicating an energy limitation for nitrogenase (C(2)H(2)) activity. In situ determinations of dinitrogen fixation in sediments also indicated low rates and exhibited a similar response to glucose amendment. Litter from the green macroalga, Ulva spp., mangrove leaves, and sea grass also gave rise to significant rates of acetylene reduction. Higher rates of nitrogenase activity (15 to 53 nmol of C(2)H(4)/g [wet weight] per h were associated with washed excised roots of three Florida mangrove species [Rhizophora mangle L., Avicennia germinans (L) Stern, and Laguncularia racemosa Gaertn.] as well as with isolated root systems of intact plants (11 to 58 mug of N/g [dry weight] per h). Following a short lag period, root-associated activity was linear and did not exhibit a marked response to glucose amendment. It appears that dinitrogen-fixing bacteria in the mangrove rhizoplane are able to use root exudates and/or sloughed cell debris as energy sources for dinitrogen fixation.

Acetylene↗
PubMed1992

Identification and cloning of Bradyrhizobium japonicum genes expressed strain selectively in soil and rhizosphere.

The growth of Bradyrhizobium japonicum USDA 110 and USDA 438 in soil extract-supplemented medium led to transcription of a large amount of DNA not expressed in basal medium. Strain USDA 438 was more competitive for the nodulation of soybean than strain USDA 110. To identify and isolate DNA regions which were expressed specifically in strain USDA 438 but not in strain USDA 110 in response to soil extract or soybean root exudate, we developed a subtractive RNA hybridization procedure. Several cosmid clones which showed strain-specific gene expression were isolated from a USDA 438 gene library. Two clones enhanced competitive nodulation when mobilized to USDA 110. The method described may be useful for identifying genes expressed in response to environmental stimuli or genes expressed differently in related microbial strains.

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↗
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↗
PubMed2025

Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production.

Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.

Solanum tuberosum↗
PubMed1977

Electronic ohmmeter. An electronic device for the determination of the root canal length.

The electronic ohmmeter was devised for the accurate determination of root canal length. Fifty-one maxillary anterior teeth of 43 patients and 25 posterior root canals from 10 patients were selected for the investigation. The presence of a lesion in periapical tissue, wide root apex, and exudates in the root canal contributed to inaccuracy in the determination of the root canal length. Correct length can be found if precautions are taken. The inaccurate results were corrected by repeating the procedures and taking precautions during the estimation of root canal length. Measurement in the dry canal gave correct estimation of the root canal length. When distilled water or normal saline was used as conducting medium in root canals, accuracy was not as good as in dry canals. The electronic ohmmeter is a useful and economical device and an endodontic aid for determination of the root canal length.

Adolescent↗
PubMedDate not supplied

Effects of flavonoids released naturally from bean (Phaseolus vulgaris) on nodD-regulated gene transcription in Rhizobium leguminosarum bv. phaseoli.

Nine flavonoid aglycones released from black bean (Phaseolus vulgaris 'PI165426CS') seeds and roots induced nodC::lacZ transcription in Rhizobium leguminosarum bv. phaseoli strains containing extra cloned copies of the regulatory genes nodD1, nodD2, or nodD3 from that biovar. Individual flavonoids generally induced highest levels of nodC::lacZ transcription (Imax) with extra copies of nodD2, and the concentration required for half-maximum induction (I50) was lowest with extra copies of nodD1 genes. One apparently unique feature of R. l. bv. phaseoli is that naturally released flavonoids with very diverse structures induce nod genes. For all three nodD genes, two compounds exuded from roots, genistein and naringenin, produced much higher levels of nodC::lacZ transcription than other flavonoids, but this fact was not explained by increased transcription of the nodD genes themselves. The remaining seven flavonoid aglycones showed reproducibly different capacities to induce nodC::lacZ transcription, but all were considerably less powerful inducers than genistein and naringenin in strains with extra copies of each of the nodD genes. Tests with glycosides of the nod-gene inducers showed that glycosides, which are normally released by bean, had lower I50 values than the corresponding aglycones with all nodD genes. Additive interactions observed between the strong nod-gene inducer genistein and the weak inducer eriodictyol remain to be explained at the molecular level.

Bacterial Proteins↗
PubMed1976

Studies on the phyllosphere microflora of tapioca (Manihot utilissima Pohl).

Studies on the phyllosphere microflora of tapioca (Manihot utilissima Pohl.) revealed that incidence of bacteria, fungi, and actinomycetes is indipendent of the variety, but dependent on the age. The bacteria and fungi increased with increasing age of the leaf and were more on mature leaves, whereas no such difference was noticed in the occurrence of actinomycetes. The large majority of the isolates, that were Gram-negative bacteria, was also amino acid-requiring. The chromogenic types occurred in greater abundance. The phyllosphere mycoflora consisted mainly of species of Asperigullus, Penicillium, Mucor, Curvularia, Alternaria, Helminthosporium, Fusarium, Hormicium, and Pullularia, at first three being predominant. There was no correlation between HCN content of leaves and microorganisms in the phyllosphere, Regarding the interrelationship between different groups of microorganisms in the phyllosphere, a positive correlation between fungi and actinomycetes and bacteria and actinomycetes in two (M. 4 and H. 105/44) varieties and a negative correlation for fungi and actinomycetes in one (H. 12/49) were obtained. The effect of leaf exudate and leaf, root, and tuber extracts on the germination of the conidia of three saprobic fungi, viz., Curvalaria sp., Alternaria sp., and Helminthosporium sp. was tested. While the leaf exudate and tuber extracts slightly stimulated the germination of the conidia of the fungi, the leaf extract exerted a selective inhibitory effect on the germination of the conidia of Curvalaria sp., but not on the conidia of Helminthosporium sp. and Alternaria sp.

Alternaria↗
PubMed1979

Protective effects of rat splenic lymphocytes and peritoneal exudate cells on herpes simplex virus infection of rat dorsal root ganglia in culture.

An in vitro model system was developed to study the effects that immune cells might have on herpes simplex virus (HSV) infection of rat dorsal root ganglia in culture. Our results demonstrate that rat splenic lymphocytes and peritoneal exudate cells are incapable of replicating HSV even if these cells come from sensitized animals and are stimulated in vitro. Both cell preparations can offer some protection to rat dorsal root ganglia from the effects of HSV infection. The data suggest that an immunologically non-specific (not mediated by sensitized cells) type of protection is important to neurons, while an immunologically specific (mediated by sensitized cells) protection is most beneficial to fibroblasts. This system can be utilized to study the mechanism of latency since the neurons of sensory ganglia are the natural site of latent herpes virus.

Animals↗
PubMed2025

Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpa.

Plants undergo physiological and metabolic changes that release specific molecules into the surrounding soil, a process collectively known as rhizodeposition. These compounds play crucial roles in plant-microbe-soil interactions, such as supporting plant development and resilience in changing environments. Under nutrient-limited conditions, these plant-derived compounds modify the rhizosphere environment, mobilizing otherwise inaccessible nutrients and recruiting stress-adaptive microbial communities that support stress resilience. Currently, the chemical diversity of rhizodeposition has yet to be fully realized but is expected to be a complex mixture that includes soluble organic compounds excreted from root cells, along with products of root cell turnover, sloughed-off root cap and border cells, and mucilage. Here, we developed a methodological and conceptual framework for an in-depth measurement of rhizodeposition through critical advancements in untargeted metabolomics. This approach provided foundational insights into the dynamic changes in rhizodeposition for the woody perennial Populus trichocarpa and rhizodeposit profiles varying by genotype, time, location, and environment. More broadly, this study provides a framework that will help formulate the next steps to effectively study rhizodeposition.

Populus↗
PubMed1992

Rhizobium nodM and nodN genes are common nod genes: nodM encodes functions for efficiency of nod signal production and bacteroid maturation.

Earlier, we showed that Rhizobium meliloti nodM codes for glucosamine synthase and that nodM and nodN mutants produce strongly reduced root hair deformation activity and display delayed nodulation of Medicago sativa (Baev et al., Mol. Gen. Genet. 228:113-124, 1991). Here, we demonstrate that nodM and nodN genes from Rhizobium leguminosarum biovar viciae restore the root hair deformation activity of exudates of the corresponding R. meliloti mutant strains. Partial restoration of the nodulation phenotypes of these two strains was also observed. In nodulation assays, galactosamine and N-acetylglucosamine could substitute for glucosamine in the suppression of the R. meliloti nodM mutation, although N-acetylglucosamine was less efficient. We observed that in nodules induced by nodM mutants, the bacteroids did not show complete development or were deteriorated, resulting in decreased nitrogen fixation and, consequently, lower dry weights of the plants. This mutant phenotype could also be suppressed by exogenously supplied glucosamine, N-acetylglucosamine, and galactosamine and to a lesser extent by glucosamine-6-phosphate, indicating that the nodM mutant bacteroids are limited for glucosamine. In addition, by using derivatives of the wild type and a nodM mutant in which the nod genes are expressed at a high constitutive level, it was shown that the nodM mutant produces significantly fewer Nod factors than the wild-type strain but that their chemical structures are unchanged. However, the relative amounts of analogs of the cognate Nod signals were elevated, and this may explain the observed host range effects of the nodM mutation. Our data indicate that both the nodM and nodN genes of the two species have common functions and confirm that NodM is a glucosamine synthase with the biochemical role of providing sufficient amounts of the sugar moiety for the synthesis of the glucosamine oligosaccharide signal molecules.

Acetylglucosamine↗
PubMed1977

Scanning microscopic evaluation of canal débridement as compared to present methods.

Ninety-one samples of root canal contents were obtained from thirty-one teeth. The paper point samples were evaluated for exudate, subjected to bacteriologic analysis, and/or examined with the scanning electron microscope. A comparison was made between the presence or absence of exudate, positive and negative cultures, and the presence or absence of contaminants as examined under the SEM. All three methods of evaluation showed some degree of correlationmscanning electron microscopy appears to be a more sensitive test for canal status.

Adolescent↗
PubMed2026

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.

BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking. RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres. CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.

Rhizosphere↗
PubMed1975

Structure and actions of saikosaponins isolated from Bupleurum falcatum L. I. Anti-inflammatory action of saikosaponins.

Anti-inflammatory action of saikosaponins isolated from the root of Bupleurum falcatum L were examined using female albino rats. The anti-exudative action by granuloma pouch method and the antigranulomatous action by cotton pellet method were demonstrated with i.m. and oral administrations of saikosaponins. The oral administration of saikosaponins in 10 times the dosage of i.m. injection showed almost the same effect. Among saikosaponins isolated from Bupleurum falcatum, saikosaponins a and d, not c, were demonstrated to have anti-inflammatory action. The relationship between structure and action of saikosaponins was discussed. No changes in body weight, adrenal weight, plasma-11-OH-corticosteroid level and hematocrit value were observed.

11-Hydroxycorticosteroids↗
PubMed1977

Surgical pocket therapy.

(1) Periodontal pockets can be treated successfully by several modalities of surgery. (2) Periodontal pocket walls do not have to be eliminated surgically in order to stop the progress of periodontal disease. (3) A residual defect which can be probed beyond 3 mm at the site of a previous peridontal pocket, does not signify a progressive lesion as long as it does not appear inflamed or contain, exudate and bleeds when probed. (4) The most important aspect of all pocket therapy is to make the exposed root surface biologically acceptable to the surrounding soft tissues. (5) The gingiva should be so closely adapted to the teeth at the end of the healing following treatment that subgingival plaque does not colonize to the extent of being recognizable clinically. (6) Frequent professional prophylaxis is of paramount importance for success of all pocket therapy.

Alveolar Process↗
PubMed2024

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model.

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Rhizosphere↗
PubMed1992

Two critical confounding factors in periodontal epidemiology.

The prevalence and severity of periodontitis is considerably lower than was previously estimated. The available epidemiological methods are based on the premise that loss of periodontal attachment is a unique sign of periodontitis. However, additional factors resulting in loss of periodontal attachment confound data obtained from modern studies. The physiological process of continuous tooth eruption results in loss of periodontal attachment over a lifetime, at an approximate rate of 0.1 mm/year. Anthropological and clinical evidence for continuous tooth eruption is reviewed. The position of the alveolar crest appears to be stable; loss of periodontal attachment occurs as the teeth erupt and less of the root is embedded in bone. Retrograde periodontitis caused by pulpal disease is a known cause of severe, localised destruction of periodontal tissues. Its signs and symptoms include periodontal pocket formation, purulent inflammatory exudates, angular bone loss, swelling and bleeding of the gingival tissues and increased tooth mobility. Anthropological, experimental and clinical evidence for retrograde periodontitis is discussed. Misdiagnosis of angular (hemiseptal), furcal and other forms of localised periodontal damage as periodontitis has probably resulted because of the inability to determine the quality of pulpal health and the assumption of a gingivitis-periodontitis continuum. New epidemiological methods need to be developed in which physiological and all pathological conditions which affect the periodontal attachment are recognised and appropriately categorised.

Confounding Factors, Epidemiologic↗