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50 results for “root nodules”
Effects of inoculation of restored and remnant prairie soils on growth, nodulation, and root colonization of three prairie legumes
In this dataset, we present legume biomass, nodule number, and % root colonization of three species of prairie legumes (Amorpha canescens, Lespedeza capitata, and Dalea purpurea) when inoculated with soil from one of 6 remnant or 10 restored prairies in southwest Michigan, USA. Plants were grown for 10 weeks in a growth chamber.
Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
<p><span>Supplementary Data 4 from the manuscript "Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants". </span></p> <p><span>A concatenated alignment of all samples and all loci. This file was used for branch length estimation and not directly for phylogeny reconstruction (though an extraction of each subtree taxonomic samples subset from this alignment would be the alignment used to produce the scaffolded subtrees that were described in the paper). Sequences are labeled by well and can be mapped back to taxon for sub-setting and further use using Supplementary Data 1. </span></p>
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton. in Spesovicornea Pacltovae Gen. Nov. Et Sp. Nov., A New Elateroid Sporomorph From The Bohemian Cenomanian (Czech Republic)
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton.
Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach
<p>There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (<i>Aspalathus linearis</i>), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread <i>Mesorhizobium</i> ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities. </p>
Convergent evolution of NFP-facilitated root nodule symbiosis
<p># NFP</p> <p>Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."</p> <p>## 00_sequences<br>This directory contains NFP/LYR homologs and annotations.</p> <p>## 02_alignments<br>This directory contains NFP alignments</p> <p>## 03_trees<br>This directory contains gene trees and species tree guides for the analyses.</p> <p>## 04_reconciliation<br>This directory contains notung files and figures for the gene tree reconciliation analysis</p> <p>## 05_synteny<br>This directory contains files for the synteny analyses. The base directory contains circos plots and a subdirectory `Synteny.2.2020` containing scripts and summary output as well as the following:<br>### Results_Apr01.zip<br>Summary of synteny results<br>### csvs.zip<br>An archive containing all csvs in the analysis.<br>### fastas.zip<br>synteny analysis - chr 5 v 8.zip<br>### tsvs.zip<br>An archive containing all csvs in the analysis.<br>### blasts.zip<br>An archive containing blast results.<br>### coords.zip<br>An archive containing genome coordinate files.<br>### gffs.zip<br>An archive containing GFF annotations.<br>### gff3s.zip<br>An archive containing GFF annotations.<br>### imgs.zip<br>An archive containing figure files used for preparing the manuscript.<br> <br>## figs<br>This directory contains figure files used for preparing the manuscript.</p> <p>## Scripts_used_CF<br>This directory contains submission and shell scripts used to conduct the analyses.</p>
Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach
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Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas
Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon-source utilization pattern, and whole-cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by 3 sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000m) had a distinctive whole-cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.
Fig. 2. 1H in Metabolite pattern in root nodules of the actinorhizal plant Casuarina equisetifolia
Fig. 2. 1H-NMR spectra of root nodule extracts of C. equisetifolia. (A) A 1H-NMR spectrum of extracts of hydrophobic compounds. (B) A 1H-NMR spectrum of extracts of hydrophilic compounds. (C) Magnified part of the 1H-NMR spectrum shown in (B). Peaks 1–6 were ascribed to tyramine, tyrosine, malate, citrate, succinate and β-glucose, respectively.
Fig. 4 in Metabolite pattern in root nodules of the actinorhizal plant Casuarina equisetifolia
Fig. 4. Growth of Frankia casuarinae strain CcI3 in BAP media with various carbon and nitrogen sources. BAP, containing 5 mM Na propionate (15 mM carbon units) as carbon source and 5 mM ammonium chloride (5 mM nitrogen units) as nitrogen source; BAP N–, BAP medium without nitrogen source; BAP C– N–, BAP medium without neither carbon nor nitrogen source; BAP C– N– + tyramine, BAP C– N– medium containing 1.875 mM tyramine (15 mM carbon units); BAP C– N– + malate, BAP C– N– medium containing 3.75 mM malate (15 mM carbon units); BAP N– + tyramine, BAP N– medium containing 5 mM tyramine (5 mM nitrogen units).
Fig. 1 in 3-Pentanol glycosides from root nodules of the actinorhizal plant Alnus cremastogyne
Fig. 1. Chemical structures of four 3-pentanol glycosides (1–4) isolated from A. cremastogyne root nodules. They are 3-pentyl β-D-glucopyranoside (1), 3-pentyl α-L- arabinofuranosyl-(1′′→6′)-β- -glucopyranoside (2), 3-pentyl α- -rhamnopyranosyl-(1′′→6′)-β- -glucopyranoside (3), and 3-pentyl 6′-(3-hydroxy3-methylglutaryl)- DLDβ-D-glucopyranoside (4).
Fig. 3 in 3-Pentanol glycosides from root nodules of the actinorhizal plant Alnus cremastogyne
Fig. 3. The contents of 3-pentanol. (A) The contents of free 3-pentanol. (B) The contents of 3-pentanol released from glycosides in various organs of A. cremastogyne. Values are in mean ± SD. Each n = 3 biological replicates.
Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas
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Data from: Silicon-induced root nodulation and synthesis of essential amino acids in a legume is associated with higher herbivore abundance
Ecologists have become increasingly aware that silicon uptake by plants, especially the Poaceae, can have beneficial effects on both plant growth and herbivore defence. The effects of silicon on other plant functional groups, such as nitrogen-fixing legumes, have been less well studied. Silicon could, however, indirectly promote herbivore performance in this group if reported increases in N2-fixation caused improvements in host plant quality for herbivores. We tested how silicon supplementation in the legume Medico sativa affected plant growth rates, root nodulation and foliage quality (silicon content and amino acid profiles) for an insect herbivore (Acyrthosiphon pisum). Plants supplemented with silicon (Si+) grew three times as quickly as those without supplementation (Si-), almost entirely in shoot mass. While root growth was unaffected by silicon uptake, root nodules containing nitrogen-fixing bacteria were 44% more abundant on Si+ plants. Aphid abundance was twice as high on Si+ plants compared to Si- plants and was positively correlated with silicon-stimulated plant growth. Si+ plants accumulated more than twice as much silicon as Si- plants, but did not have higher silicon concentrations because of dilution effects linked to the rapid growth of Si+ plants. Si+ plants showed a 65% increase in synthesis of essential foliar amino acids, probably due to increased levels of root nodulation. These results suggest that increased silicon supply makes M. sativa more susceptible to A. pisum, mainly because of increased plant growth and resource availability (i.e. essential amino acids). While silicon augmentation of the Poaceae frequently improves herbivore defence, the current study illustrates that this cannot be assumed for other plant families where the beneficial effects of silicon on plant growth and nutrition may promote herbivore performance in some instances.
Fig. 1 in Metabolite pattern in root nodules of the actinorhizal plant Casuarina equisetifolia
Fig. 1. The chemical structure (left) and key HMBC correlations (from H to C, right) of compound 1.
Fig. 2 in 3-Pentanol glycosides from root nodules of the actinorhizal plant Alnus cremastogyne
Fig. 2. Key heteronuclear multiple bond correlations of compounds 2–4.
Data from: Silicon-induced root nodulation and synthesis of essential amino acids in a legume is associated with higher herbivore abundance
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Processing of NODULE INCEPTION controls transition to nitrogen fixation in root nodules
GEO Series GSE178119. Medicago truncatula. 23 samples. Type: Expression profiling by high throughput sequencing.
Overproduction of indole-3-acetic acid in free-living rhizobia mimics physiological conditions required for nitrogen fixation inside root nodules
GEO Series GSE69880. Sinorhizobium meliloti. 6 samples. Type: Expression profiling by high throughput sequencing.
Metabolomic profiling of Bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures
GEO Series GSE79811. Bradyrhizobium diazoefficiens; Bradyrhizobium diazoefficiens USDA 110. 6 samples. Type: Expression profiling by array.
Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.
GEO Series GSE104582. Glycine max. 12 samples. Type: Expression profiling by array.
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