School of BioSciences - Research Publications
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ItemDiscovery of novel neutral glycosphingolipids in cereal crops: rapid profiling using reversed-phased HPLC-ESI-QqTOF with parallel reaction monitoring(Nature Portfolio, 2023-12-19)This study explores the sphingolipid class of oligohexosylceramides (OHCs), a rarely studied group, in barley (Hordeum vulgare L.) through a new lipidomics approach. Profiling identified 45 OHCs in barley (Hordeum vulgare L.), elucidating their fatty acid (FA), long-chain base (LCB) and sugar residue compositions; and was accomplished by monophasic extraction followed by reverse-phased high performance liquid chromatography electrospray ionisation quadrupole-time-of-flight tandem mass spectrometry (HPLC-ESI-QqTOF-MS/MS) employing parallel reaction monitoring (PRM). Results revealed unknown ceramide species and highlighted distinctive FA and LCB compositions when compared to other sphingolipid classes. Structurally, the OHCs featured predominantly trihydroxy LCBs associated with hydroxylated FAs and oligohexosyl residues consisting of two-five glucose units in a linear 1 → 4 linkage. A survey found OHCs in tissues of major cereal crops while noting their absence in conventional dicot model plants. This study found salinity stress had only minor effects on the OHC profile in barley roots, leaving questions about their precise functions in plant biology unanswered.
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ItemNo Preview AvailableDeciphering the Interactions in the Root-Soil Nexus Caused by Urease and Nitrification Inhibitors: A Review(MDPI, 2023-06)Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH3) volatilization, nitrous oxide emissions, denitrification, nitrate (NO3−) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH4+) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH4+ and reduce nitrogen loss through NH3 volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH4+ to nitrite (NO2−), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO3− or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.
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ItemAssessing the Efficacy, Acute Toxicity, and Binding Modes of the Agricultural Nitrification Inhibitors 3,4-Dimethyl-1H-pyrazole (DMP) and Dicyandiamide (DCD) with Nitrosomonas europaea(American Chemical Society, 2023-01-25)Nitrification inhibitors have been coformulated with nitrogen fertilizers since the 1970s to modulate the microbiological conversion of nitrogen in agricultural soils. 3,4-Dimethyl-1H-pyrazole (DMP) and dicyandiamide (DCD) are currently the most used commercial nitrification inhibitors, but their mode of action is not well understood. This work seeks to fill this void by assessing for the first time in detail their mechanism of inhibition, efficacy, and acute toxicity with pure cell cultures of Nitrosomonas europaea. Bacterial assays based on the quantification of the nitrite (NO2–) production showed that both inhibitors reversibly target ammonia monooxygenase (AMO), which catalyzes the first step of the nitrification process. Michaelis–Menten kinetics suggest that both DMP and DCD act as uncompetitive inhibitors. Real-time measurements of the oxygen (O2) consumption confirmed the nonmechanistic mode of inhibition and showed that DMP reduced the O2 uptake rate by AMO much more at considerably lower concentrations than DCD, in line with the lower inhibitory efficiency of the latter. Acute toxicity tests revealed that DCD has a 10% higher toxicity than DMP when comparing treatments at the same inhibition efficacy (i.e., DMP at 10 ppm, DCD at 100 ppm), indicating that the inhibition of the nitrification process cannot simply be achieved by increasing the inhibitor concentration. The methods presented in this study could assist the development of more reliable nitrification inhibitors in the future.
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ItemFunctional Traits 2.0: The power of the metabolome for ecology(WILEY, 2022-01)Abstract A major aim of ecology is to upscale attributes of individuals to understand processes at population, community and ecosystem scales. Such attributes are typically described using functional traits, that is, standardised characteristics that impact fitness via effects on survival, growth and/or reproduction. However, commonly used functional traits (e.g. wood density, SLA) are becoming increasingly criticised for not being truly mechanistic and for being questionable predictors of ecological processes. This Special Feature reviews and studies how the metabolome (i.e. the thousands of unique metabolites that underpin physiology) can enhance trait‐based ecology and our understanding of plant and ecosystem functioning. In this Editorial, we explore how the metabolome relates to plant functional traits, with reference to life‐history trade‐offs governing fitness between generations and plasticity shaping fitness within generations. We also identify solutions to challenges of acquiring, interpreting and contextualising metabolome data, and propose a roadmap for integrating the metabolome into ecology. We next summarise the seven studies composing the Special Feature, which use the metabolome to examine mechanisms behind plant community assembly, plant‐organismal interactions and effects of plants and soil micro‐organisms on ecosystem processes. Synthesis. We demonstrate the potential of the metabolome to improve mechanistic and predictive power in ecology by providing a high‐resolution coupling between physiology and fitness. However, applying metabolomics to ecological questions is currently limited by a lack of conceptual, technical and data frameworks, which needs to be overcome to realise the full potential of the metabolome for ecology.
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ItemPlant Growth Promotion and Heat Stress Amelioration in Arabidopsis Inoculated with Paraburkholderia phytofirmans PsJN Rhizobacteria Quantified with the GrowScreen-Agar II Phenotyping Platform(MDPI, 2022-11)High temperatures inhibit plant growth. A proposed strategy for improving plant productivity under elevated temperatures is the use of plant growth-promoting rhizobacteria (PGPR). While the effects of PGPR on plant shoots have been extensively explored, roots-particularly their spatial and temporal dynamics-have been hard to study, due to their below-ground nature. Here, we characterized the time- and tissue-specific morphological changes in bacterized plants using a novel non-invasive high-resolution plant phenotyping and imaging platform-GrowScreen-Agar II. The platform uses custom-made agar plates, which allow air exchange to occur with the agar medium and enable the shoot to grow outside the compartment. The platform provides light protection to the roots, the exposure of it to the shoots, and the non-invasive phenotyping of both organs. Arabidopsis thaliana, co-cultivated with Paraburkholderia phytofirmans PsJN at elevated and ambient temperatures, showed increased lengths, growth rates, and numbers of roots. However, the magnitude and direction of the growth promotion varied depending on root type, timing, and temperature. The root length and distribution per depth and according to time was also influenced by bacterization and the temperature. The shoot biomass increased at the later stages under ambient temperature in the bacterized plants. The study offers insights into the timing of the tissue-specific, PsJN-induced morphological changes and should facilitate future molecular and biochemical studies on plant-microbe-environment interactions.
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ItemNo Preview AvailableRapid and Inexpensive Assay for Testing the Efficiency of Potential New Synthetic Nitrification Inhibitors(AMER CHEMICAL SOC, 2023-03-20)
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ItemRoot Growth and Architecture of Wheat and Brachypodium Vary in Response to Algal Fertilizer in Soil and Solution(MDPI, 2022-02)Alternative, recycled sources for mined phosphorus (P) fertilizers are needed to sustain future crop growth. Quantification of phenotypic adaptations and performance of plants with a recycled nutrient source is required to identify breeding targets and agronomy practices for new fertilization strategies. In this study, we tested the phenotypic responses of wheat (Triticum aestivum) and its genetic model, Brachypodium (Brachypodium distachyon), to dried algal biomass (with algae or high or low mineral P) under three growing conditions (fabricated ecosystems (EcoFABs), hydroponics, and sand). For both species, algal-grown plants had similar shoot biomass to mineral-grown plants, taking up more P than the low mineral P plants. Root phenotypes however were strongly influenced by nutrient form, especially in soilless conditions. Algae promoted the development of shorter and thicker roots, notably first and second order lateral roots. Root hairs were 21% shorter in Brachypodium, but 24% longer in wheat with algae compared to mineral high P. Our results are encouraging to new recycled fertilization strategies, showing algae is a nutrient source to wheat and Brachypodium. Variation in root phenotypes showed algal biomass is sensed by roots and is taken up at a higher amount per root length than mineral P. These phenotypes can be selected and further adapted in phenotype-based breeding for future renewal agriculture systems.
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ItemEditorial: Salinity tolerance: From model or wild plants to adapted crops(FRONTIERS MEDIA SA, 2022-07-27)
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ItemBiochemical Changes in Two Barley Genotypes Inoculated With a Beneficial Fungus Trichoderma harzianum Rifai T-22 Grown in Saline Soil(FRONTIERS MEDIA SA, 2022-08-02)One of the most important environmental factors impacting crop plant productivity is soil salinity. Fungal endophytes have been characterised as biocontrol agents that help in plant productivity and induce resistance responses to several abiotic stresses, including salinity. In the salt-tolerant cereal crop barley (Hordeum vulgare L.), there is limited information about the metabolites and lipids that change in response to inoculation with fungal endophytes in saline conditions. In this study, gas chromatography coupled to mass spectrometry (GC-MS) and LC-electrospray ionisation (ESI)-quadrupole-quadrupole time of flight (QqTOF)-MS were used to determine the metabolite and lipid changes in two fungal inoculated barley genotypes with differing tolerance levels to saline conditions. The more salt-tolerant cultivar was Vlamingh and less salt tolerant was Gairdner. Trichoderma harzianum strain T-22 was used to treat these plants grown in soil under control and saline (200 mM NaCl) conditions. For both genotypes, fungus-colonised plants exposed to NaCl had greater root and shoot biomass, and better chlorophyll content than non-colonised plants, with colonised-Vlamingh performing better than uninoculated control plants. The metabolome dataset using GC-MS consisted of a total of 93 metabolites of which 74 were identified in roots of both barley genotypes as organic acids, sugars, sugar acids, sugar alcohols, amino acids, amines, and a small number of fatty acids. LC-QqTOF-MS analysis resulted in the detection of 186 lipid molecular species, classified into three major lipid classes-glycerophospholipids, glycerolipids, and sphingolipids, from roots of both genotypes. In Cultivar Vlamingh both metabolites and lipids increased with fungus and salt treatment while in Gairdner they decreased. The results from this study suggest that the metabolic pathways by which the fungus imparts salt tolerance is different for the different genotypes.