Michelle Watt

OpenSimRoot: widening the scope and application of root architectural models

Summary OpenSimRoot is an open‐source, functional–structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of simroot, established to simulate root system architecture, nutrient acquisition and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate the following: resource costs of developmental and anatomical traits; trait synergisms; and (interspecies) root competition. OpenSimRoot can model three‐dimensional images from magnetic resonance imaging (MRI) and X‐ray computed tomography (CT) of roots in soil. New modules include: soil water‐dependent water uptake and xylem flow; tiller formation; evapotranspiration; simultaneous simulation of mobile solutes; mesh refinement; and root growth plasticity. OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and to gain a mechanistic understanding at system scales.

GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system based on germination paper to quantify crop phenotypic diversity and plasticity of root traits under varying nutrient supply

New techniques and approaches have been developed for root phenotyping recently; however, rapid and repeatable non-invasive root phenotyping remains challenging. Here, we present GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system (4 plants min-1) based on flat germination paper. GrowScreen-PaGe allows the acquisition of time series of the developing root systems of 500 plants, thereby enabling to quantify short-term variations in root system. The choice of germination paper was found to be crucial and paper☓root interaction should be considered when comparing data from different studies on germination paper. The system is suitable for phenotyping dicot and monocot plant species. The potential of the system for high-throughput phenotyping was shown by investigating phenotypic diversity of root traits in a collection of 180 rapeseed accessions and of 52 barley genotypes grown under control and nutrient-starved conditions. Most traits showed a large variation linked to both genotype and treatment. In general, root length traits contributed more than shape and branching related traits in separating the genotypes. Overall, results showed that GrowScreen-PaGe will be a powerful resource to investigate root systems and root plasticity of large sets of plants and to explore the molecular and genetic root traits of various species including for crop improvement programs.

Root hairs enable high transpiration rates in drying soils

Do root hairs help roots take up water from the soil? Despite the well-documented role of root hairs in phosphate uptake, their role in water extraction is controversial. We grew barley (Hordeum vulgare cv Pallas) and its root-hairless mutant brb in a root pressure chamber, whereby the transpiration rate could be varied whilst monitoring the suction in the xylem. The method provides accurate measurements of the dynamic relationship between the transpiration rate and xylem suction. The relationship between the transpiration rate and xylem suction was linear in wet soils and did not differ between genotypes. When the soil dried, the xylem suction increased rapidly and non-linearly at high transpiration rates. This response was much greater with the brb mutant, implying a reduced capacity to take up water. We conclude that root hairs facilitate the uptake of water by substantially reducing the drop in matric potential at the interface between root and soil in rapidly transpiring plants. The experiments also reinforce earlier observations that there is a marked hysteresis in the suction in the xylem when the transpiration rate is rising compared with when it is falling, and possible reasons for this behavior are discussed.

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

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.

Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics

Protein post-translational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined.