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179 results for “Rhizosphere”
Data from: The effect of rhizosphere microbes outweighs host plant genotype in reducing insect herbivory
Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae. The population with lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.) attack; no association was observed between GLS and damage by a second herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (disrupted vs. intact native microbiome) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted vs. intact native microbiome treatment. These differences may be attributable to shifts in primary metabolic pathways previously implicated in host defense against herbivores, including increases in pentose and glucoronate interconversion among plants grown with an intact microbiome. Further, native microbiomes with distinct community composition (as estimated from 16s rRNA amplicon sequencing) differed 2-fold in their effect on host plant susceptibility to aphids. The findings suggest that rhizosphere microbes, including distinct native microbiomes, can play a greater role than plant genotype in defense against insect herbivores, and act through metabolic mechanisms independent of plant genotype.
Data from: Switchgrass rhizosphere metabolite chemistry driven by nitrogen availability
<p>Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (<i>Panicum virgatum</i>) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. Plants were grown with the inoculum <i>Azotobacter vinelandii</i> DJ for three days before harvest. We found switchgrass root exudate chemistry to be driven by N availability. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment. However, we found little evidence of N treatment and inoculation interaction effects which suggests this response is not directly mediated by N availability.</p>
Nitrogen fixation and crop productivity enhancements codriven by intercrop root exudates and key rhizosphere bacteria
<p>1. Crop diversity management is widely used to increase agricultural productivity and sustainability. Recent studies have demonstrated that maize root exudates can drive interspecific facilitation to enhance N<sub>2</sub> fixation of bean in intercropping systems. However, the mechanisms of N<sub>2</sub> fixation enhancement stimulated by root exudates in the intercropping systems remain unclear.</p> <p>2. Four experiments were designed to provide a progressively deeper understanding of how root exudates stimulate microbial-mediated N<sub>2</sub> fixation. First, the effects of faba bean/maize intercropping on yields and soil microbial communities were determined in a field experiment. Second, root-derived interspecific facilitation was evaluated using a root partitioning approach. Third, the key microbial taxa in the faba bean rhizosphere were traced using<sup> 13</sup>C-labeled maize root exudates. Fourth, the codriven mechanism of maize root exudates and microorganisms in the faba bean rhizosphere were explored.</p> <p>3. Faba bean/maize intercropping with maize residue return increased the yields of faba bean (26%), maize (27%), and broccoli (9.1%) compared to that under monocropping. Nodulin-like 4 (NODL4), chalcone-flavanone isomerase (CFI), and early nodulin-like (ENODL2) gene expression in faba bean roots intercropped with maize increased by 1.5-2.3-fold compared to that observed under monoculture. More than half of the N<sub>2</sub> fixation of faba bean increase under intercropping was due to interactions with microorganisms. Nine key bacterial genera in the faba bean rhizosphere were identified by <sup>13</sup>C-DNA based stable isotope probing analysis. Among them <i>Agromyces</i>, <i>Arthrobacter</i>, <i>Bacillus</i>, <i>Lysobacter</i>, and <i>Paenibacillus</i> directly fix N<sub>2</sub>, while <i>Gemmatimonas</i>, <i>Heliobacillus</i>, <i>Natronocella</i>, and <i>Sorangium</i> increase the N<sub>2</sub> fixation capacity of Azotobacter by providing additional carbon sources. These key bacteria triggered by maize root exudates played an important role in the rhizosphere facilitation of intercropping.</p> <p>4. <i>Synthesis and applications</i>. We demonstrated a novel root-root facilitation of N<sub>2</sub> fixation and increased crop yields codriven by root exudates and rhizosphere bacteria under faba bean/maize intercropping, and nine key bacteria associated with this process were identified by <sup>13</sup>C-DNA based stable isotope probing. We recommend the adoption and optimization of intercropping systems with residue return to reduce the shortcomings of continuous cropping and to increase the sustainability of crop <a>production</a>.</p>
FIGURE 2 in Stagonosporopsis rhizophilae sp. nov. (Didymellaceae, Pleosporales), a new rhizospheric soil fungus associated with Populus deltoides Marsh
FIGURE 2. Stagonosporopsis rhizophilae sp. nov. (CGMCC3.19852). A–D. Colonies on PDA, MEA, CA, and OA, respectively (front and reverse); E. Pycnidia forming on OA. F. Section of pycnidium. G. Section of pycnidial wall. H. Conidiogenous cells. I. Conidia. Scale bars: 800 μm (E), 20 μm (F), 10 μm (G–I). PDA: potato dextrose agar, MEA: malt extract agar, CA: cherry-decoction agar, and OA: oatmeal agar.
Fig. 1 in Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima
Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of strain XAAS-2T and close relatives. Bootstrap values (1000 replications) above 50 % are showed at nodes. Asterisks indicate that the corresponding nodes were also recovered in the maximum-likelihood and maximum-evolution trees. Bar, 0.01 substitutions per nucleotide position.
Fig. 1 in Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower)
Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationships of the stain Deinococcus hibisci THG-AG1.5T with the related species. Filled circles at nodes indicate branches that were also recovered by using the maximumparsimony algorithm. Bootstrap values (expressed as percentage of 1000 replications) over 70 % are shown at the branching points. Bar, 0.01 substitutions per nucleotide position.
Fig. 1 in Saccharopolyspora rhizosphaerae sp. nov., an actinomycete isolated from rhizosphere soil in Thailand
Fig. 1. Neighbour-joining phylogenetic tree based on the 16S rRNA gene sequences, showing the genetic relatedness between strain H219T and other type strains in the genus Saccharopolyspora. Streptosporangium roseum DSM 43021T (NR074558) was used as the outgroup. Bootstrap values above 50 % or higher (percentages of 1000 replications) are shown. Bar, 0.01 substitutions per nucleotide position. Filled circles indicate branches that are also recovered in the maximum-parsimony and the maximum-likelihood trees (see Figs S3 and S4).
Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time
<p>This is a supplementary material for the article of "Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time"</p>
FIGURE 3. A in Trichoderma bombaxalis sp. nov., isolated from rhizosphere soils of Lycium barbarum
FIGURE 3. A. Cultures at 25 °C after 7 days on xylan medium. B. Following Congo red dyeing and decolorization on xylan medium. C. Cultures at 25 °C after 7 days on CMC-Na medium. D. Following Congo red dyeing and decolorization on CMC-Na medium.
FIGURE 1 in Trichoderma bombaxalis sp. nov., isolated from rhizosphere soils of Lycium barbarum
FIGURE 1. Phylogenetic tree based on maximum likelihood analysis of the combined ITS, RPB2 and TEF1-a dataset. Trichoderma protrudens and T. turrialbense are the outgroup taxa. Bootstrap values higher than 70% from RAxML (MPBP) (left) and Bayesian posterior probabilities greater than 0.95 (BIPP) (right) are given above the nodes. Asterisks indicate bootstrap values of less than 70% or Bayesian posterior probabilities lower than 0.95.T indicates ex-type isolates; isolates obtained in this study are in red.
Images of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation"
<p>These images are the images of zymography, <sup>14</sup>C imaging and neutron radiography of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation". Raw data on optimal water conditions were partially overlapping with the data of Bilyera et al., 2021, Soil Biology and Biochemistry, 162, 108426.</p>
dataset of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation"
<p>This is the dataset of the enzyme kinetics, and other biochemical properties obtained from zymography, <sup>14</sup>C images and water images of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation". </p>
Impact of Rhizosphere Quantitative Microbiome and Soil Properties on Alkaloid Dynamics in Lycoris aurea
Open the record for dataset details and reuse information.
Impact of transgenic maize Ruifeng125 on diversity and dy-namics of bacterial community in rhizosphere soil
<p><span>With the development of commercialized planting of genetically modified crops, their ecological security risks remain a hot topic of public concern. Insect-resistant genetically modified maize Ruifeng125 which expressing a fusion Bt protein (Cry1Ab-Cry2Aj) has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected firstly. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw returning to the field, over 97% of Bt proteins has been degraded quickly at the early stages (≤ 10 d) and then they were degraded at a relative slow rate. In addition, the variations of bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families and 842 genera were obtained by 16S rRNA sequencing, among which <em>Proteobacteria</em>, <em>Actinobacia</em>, <em>Acidobacter</em> <em>Acidobacterium</em> and <em>Chloroflexi</em> were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution for the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establish a theoretical foundation for their environmental safety assessment.</span></p>
Data from: Exploring actinobacteria associated with rhizosphere and endosphere of the native Alpine medicinal plant Leontopodium nivale Subspecies alpinum
<p>The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pretreatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.</p>
Data from: Site specific distribution of oak rhizosphere associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and P. cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud-F (Hudspeth, Nadler, & Hudspeth, 2000) and a reverse primer found using DegePrime (Hugerth et al., 2014). Factors reflecting topo-edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and Phytophthora cinnamomi, both displaying strong site specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlights the importance to study oomycete communities in relation to such ecological patterns.
FIGURE 2 in Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil
FIGURE 2. Phylogram constructed from sequences for the ITS region of rDNA showing the phylogenetic position of Corniculariella brasiliensis. Erysiphe pisi was used as the outgroup. Sequences are labeled with their database accession numbers Thick branches in grey represent clades
FIGURE 3. Corniculariella brasiliensis. Micromorphological characters. a Conidia 1-septate. b Conidiogenous cells phialidic. c in Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil
FIGURE 3. Corniculariella brasiliensis. Micromorphological characters. a Conidia 1-septate. b Conidiogenous cells phialidic. c Conidiomata eustromatic immersed in the culture medium.
FIGURE 1 in Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil
FIGURE 1. Phylogram constructed from partial sequences for LSU rDNA showing the phylogenetic position of Corniculariella brasiliensis. Ceratocystiopsis ranaculosa and Ambrosiella ferruginea were used as the outgroup. Sequences are labeled with their database accession numbers. Support values are for Bayesian inference and maximum likelihood analyses (values above and below the branches, respectively). Thick branches in grey represent clades with 90% bootstrap support in all analyses. Sequences obtained in this study are in
FIGURE 3 in Description of Neodolichodorus hainanensis n. sp. (Nematoda: Dolichodoridae) from rhizosphere soil of golf turf in China
FIGURE 3. SEM micrographs of N. hainanensis n. sp. A, B. Lip region of female in lateral view; C. Lateral field; D, E. Male tails in lateral view.
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