scholarly journals Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

2018 ◽  
Author(s):  
Joelle Sasse ◽  
Josefine Kant ◽  
Benjamin J Cole ◽  
Andrew P Klein ◽  
Borjana Arsova ◽  
...  
Keyword(s):  
Plant Traits ◽  
Brachypodium Distachyon ◽  
Root Hairs ◽  
Plant Morphology ◽  
Growth Conditions ◽  
Soil Extract ◽  
Physiochemical Properties ◽  
Experimental Treatments ◽  
Model Grass ◽  
Soil Influence

There is a dynamic reciprocity between plants and their environment: On one hand, the physiochemical properties of soil influence plant morphology and metabolism, while on the other, root morphology and exudates shape the environment surrounding roots. Here, we investigate both of these aspects as well as the reproducibility of these responses across laboratories. The model grass Brachypodium distachyon was grown in phosphate-sufficient and phosphate-deficient mineral media, as well as in sterile soil extract, within fabricated ecosystem (EcoFAB) devices across four laboratories. Tissue weight and phosphate content, total root length, root tissue and exudate metabolic profiles were found to be consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct in all laboratories, with root hairs four times longer compared to other growth conditions. Further, plants depleted half of the investigated metabolites from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures; they also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high inter-laboratory reproducibility, demonstrating that their value in standardized investigations of plant traits.

scholarly journals Root morphology and exudate availability is shaped by particle size and chemistry in Brachypodium distachyon

2019 ◽  
Author(s):  
Joelle Sasse ◽  
Jacob S. Jordan ◽  
Markus DeRaad ◽  
Katherine Whiting ◽  
Katherina Zhalnina ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Particle Size ◽  
Root Morphology ◽  
Brachypodium Distachyon ◽  
Root Exudation ◽  
Plant Morphology ◽  
Glass Beads ◽  
Substrate Size ◽  
Model Grass ◽  
Sphere Of Influence

AbstractRoot morphology and exudation define a plants sphere of influence in soils, and are in turn shaped by the physiochemical characteristics of soil. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of the model grass Brachypodium distachyon. Root fresh weight and root lengths were correlated with particle size, whereas root number and shoot weight remained constant. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate metabolite profiles detected with liquid chromatography / mass spectrometry were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay. However, when exudates of clay-grown plants were collected by removing the plants from the substrate, their exudate profile was similar to sand- or glass beads-grown plants. Clay particles sorbed 20% of compounds exuded by clay-grown plants, and 70% of compounds of a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides/nucleotides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be de-sorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. We show that root morphology is affected by substrate size, and that root exudation in contrast is not affected by substrate size or chemistry. The availability of exuded compounds, however, depends on the substrate present. These findings further support the critical importance of the physiochemical properties of soils are crucial to consider when investigating plant morphology, exudation, and plant-microbe interactions.

scholarly journals Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

2020 ◽  
Vol 21 (18) ◽  
pp. 6700
Author(s):  
Aleksandra Skalska ◽  
Christoph Stritt ◽  
Michele Wyler ◽  
Hefin W. Williams ◽  
Martin Vickers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brachypodium Distachyon ◽  
Growth Conditions ◽  
Grass Species ◽  
Niche Modelling ◽  
Climate Niche ◽  
Population Structure Analysis ◽  
Delayed Flowering ◽  
Model Grass ◽  
The Uk

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.

scholarly journals 3,4-dehydro-L-proline Induces Programmed Cell Death in the Roots of Brachypodium distachyon

2021 ◽  
Vol 22 (14) ◽  
pp. 7548
Author(s):  
Artur Pinski ◽  
Alexander Betekhtin ◽  
Jolanta Kwasniewska ◽  
Lukasz Chajec ◽  
Elzbieta Wolny ◽  
...  
Keyword(s):  
Cell Death ◽  
Brachypodium Distachyon ◽  
Root Hairs ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Cell Wall Proteins ◽  
Root Epidermis ◽  
Root Hair Development ◽  
Transmission Electron ◽  
Hair Development

As cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs) take part in plant growth and various developmental processes. To fulfil their functions, HRGPs, extensins (EXTs) in particular, undergo the hydroxylation of proline by the prolyl-4-hydroxylases. The activity of these enzymes can be inhibited with 3,4-dehydro-L-proline (3,4-DHP), which enables its application to reveal the functions of the HRGPs. Thus, to study the involvement of HRGPs in the development of root hairs and roots, we treated seedlings of Brachypodium distachyon with 250 µM, 500 µM, and 750 µM of 3,4-DHP. The histological observations showed that the root epidermis cells and the cortex cells beneath them ruptured. The immunostaining experiments using the JIM20 antibody, which recognizes the EXT epitopes, demonstrated the higher abundance of this epitope in the control compared to the treated samples. The transmission electron microscopy analyses revealed morphological and ultrastructural features that are typical for the vacuolar-type of cell death. Using the TUNEL test (terminal deoxynucleotidyl transferase dUTP nick end labelling), we showed an increase in the number of nuclei with damaged DNA in the roots that had been treated with 3,4-DHP compared to the control. Finally, an analysis of two metacaspases’ gene activity revealed an increase in their expression in the treated roots. Altogether, our results show that inhibiting the prolyl-4-hydroxylases with 3,4-DHP results in a vacuolar-type of cell death in roots, thereby highlighting the important role of HRGPs in root hair development and root growth.

scholarly journals Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon

2011 ◽  
Vol 193 (2) ◽  
pp. 376-386 ◽  
Author(s):  
José M. Barrero ◽  
John V. Jacobsen ◽  
Mark J. Talbot ◽  
Rosemary G. White ◽  
Stephen M. Swain ◽  
...  
Keyword(s):  
Light Quality ◽  
Brachypodium Distachyon ◽  
Grain Dormancy ◽  
Model Grass

scholarly journals Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus

2018 ◽  
Vol 93 (6) ◽  
pp. 1088-1101 ◽  
Author(s):  
Yinjia Li ◽  
Sheng Zuo ◽  
Zhiliang Zhang ◽  
Zhanjie Li ◽  
Jinlei Han ◽  
...  
Keyword(s):  
Brachypodium Distachyon ◽  
Centromeric Dna ◽  
Dna Characterization ◽  
Model Grass

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 152-163 ◽  
Author(s):  
Mirko Barbieri ◽  
Thierry C. Marcel ◽  
Rients E. Niks ◽  
Enrico Francia ◽  
Marianna Pasquariello ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Rust Fungus ◽  
Brachypodium Distachyon ◽  
Transgressive Segregation ◽  
Snp Markers ◽  
Growth Stages ◽  
Resistance Qtls ◽  
Ssr And Snp Markers ◽  
Model Grass ◽  
Genomic Regions

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

scholarly journals Brachypodium distachyon–Cochliobolus sativus Pathosystem is a New Model for Studying Plant–Fungal Interactions in Cereal Crops

2015 ◽  
Vol 105 (4) ◽  
pp. 482-489 ◽  
Author(s):  
Shaobin Zhong ◽  
Shaukat Ali ◽  
Yueqiang Leng ◽  
Rui Wang ◽  
David F. Garvin
Keyword(s):  
Molecular Mechanisms ◽  
Brachypodium Distachyon ◽  
Bipolaris Sorokiniana ◽  
Transgressive Segregation ◽  
Cochliobolus Sativus ◽  
Cereal Crops ◽  
New Model ◽  
Model Grass ◽  
Fungal Interactions ◽  
Important Disease

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) causes spot blotch, common root rot, and kernel blight or black point in barley and wheat. However, little is known about the molecular mechanisms underlying the pathogenicity of C. sativus or the molecular basis of resistance and susceptibility in the hosts. This study aims to establish the model grass Brachypodium distachyon as a new model for studying plant–fungus interactions in cereal crops. Six B. distachyon lines were inoculated with five C. sativus isolates. The results indicated that all six B. distachyon lines were infected by the C. sativus isolates, with their levels of resistance varying depending on the fungal isolates used. Responses ranging from hypersensitive response-mediated resistance to complete susceptibility were observed in a large collection of B. distachyon (2n = 2x = 10) and B. hybridum (2n = 4x = 30) accessions inoculated with four of the C. sativus isolates. Evaluation of an F2 population derived from the cross between two of the B. distachyon lines, Bd1-1 and Bd3-1, with isolate Cs07-47-1 showed quantitative and transgressive segregation for resistance to C. sativus, suggesting that the resistance may be governed by quantitative trait loci from both parents. The availability of whole-genome sequences of both the host (B. distachyon) and the pathogen (C. sativus) makes this pathosystem an attractive model for studying this important disease of cereal crops.

Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon

2011 ◽  
Vol 123 (3) ◽  
pp. 455-464 ◽  
Author(s):  
Naxin Huo ◽  
David F. Garvin ◽  
Frank M. You ◽  
Stephanie McMahon ◽  
Ming-Cheng Luo ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Brachypodium Distachyon ◽  
High Density ◽  
Genome Features ◽  
Model Grass

Factors affecting adsorption of Azospirillum brasilense Cd to root hairs as compared with root surface of wheat

1989 ◽  
Vol 35 (10) ◽  
pp. 936-944 ◽  
Author(s):  
Yoav Bashan ◽  
Hanna Levanony
Keyword(s):  
Azospirillum Brasilense ◽  
Root Hairs ◽  
Growth Conditions ◽  
Root Surface ◽  
Logarithmic Phase ◽  
Bacterial Cells ◽  
Beneficial Bacteria ◽  
Factors Affecting ◽  
Associative Bacteria ◽  
Bacterial Adsorption

Electron microscopy of wheat (Triticum aestivum) roots inoculated with Azospirillum brasilense Cd revealed massive adsorption of bacterial cells to the root surface and less adsorption to root hairs. Quantitative analysis of A. brasilense Cd adsorption to root surface and to root hairs, confirmed qualitatively by light microscopy observations, revealed a bacterial adsorption ratio of 5 (+2): 1 (root surface: root hairs). Extreme bacterial adsorption ratios were recorded when bacteria were previously grown in the presence of KNO3 (27:1) or when bacterial cells were inoculated under hydroponic plant growth conditions (80:1). Adsorption of A. brasilense Cd to roots was directly related to the bacterial growth phase, with logarithmic phase cultures demonstrating a greater adsorption than stationary phase cultures. Adsorption to root hairs was dependent mainly on the number of root hairs developed under certain growth conditions. When very few root hairs had developed, most of the bacterial cells were adsorbed to the root surface. Factors such as starvation, bacteria grown in culture in the presence of KNO3, addition of several nutrients, and protease or NaEDTA treatments of bacterial cells before the adsorption assay decreased bacterial adsorption to root hairs. Other factors such as microaerophilic growth conditions, addition of several bacterial chemoattractants, and cellulase-treated root hairs enhanced bacterial adsorption. It is proposed that although A. brasilense Cd adsorbed to every part of the root system, more cells adsorbed to the root surface of wheat than to the root hairs.Key words: associative bacteria, Azospirillum, bacterial adsorption, beneficial bacteria, rhizosphere bacteria, root-hair colonization.

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