Biology subjects

Roessner, U.

Publications and source records attributed to Roessner, U..

13 recordsLinked to original sources

bioRxiv2025

Systems-level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation

Plant molecular adaptation to plant growth promoting bacteria (PGPB) under nutrient stress remains unclear, yet is essential for advancing PGPB use in agriculture. The model grass Brachypodium dystachion was studied together with Pseudomonas koreeensis (Pk) at two nitrogen (N) conditions. Non-invasive shoot phenotyping showed an immediate response to low-N, while beneficial effects of Pk became quantifiable after day 19. Increased N content in inoculated plants, along with Pks ability to grow on N-free media, suggests bacterial N contribution at deficient N. In low-N conditions, Pk-inoculated plants showed 33.2% more N than uninoculated controls and biomass comparable to high-N plants. Pk had no effect under sufficient N. Proteomics and lipidomics revealed that lipid profiles were primarily shaped by N availability, while protein abundance responded to both Pk and N status. Inoculated low-N plants displayed protein profiles resembling those of high-N controls, with some distinct exceptions. The plant-microbe interaction is dynamic and developed over 3 weeks, leading to increased biomass and N content. Root proteins strongly induced by Pk under low-N included lipid degradation enzymes, N transporters, and regulatory proteins, suggesting a coordinated remodelling of energy metabolism supporting whole-plant biomass and increased abundance of N uptake proteins.

plant biology↗

bioRxiv2025

Thermotolerance in Chia (Salvia hispanica L.) is Mediated by Rapid Heat-Induced Transcriptomic Reprogramming and Lipid Remodelling in Leaves

Heat stress poses a significant threat to crop productivity; however, the thermotolerance mechanisms in underutilised oilseed crops, such as chia (Salvia hispanica L.), remain poorly understood. Despite the growing interest in chia as a rich source of {omega}-3 fatty acids, its molecular response to heat stress, particularly in vegetative tissues, has not been explored. We conducted transcriptomic and lipidomic profiling to examine how chia leaves respond to short-term (3 h) and prolonged (27 h) heat stress, followed by recovery under ambient conditions. Heat stress induced differential expression in over 20% of transcripts in chia leaves, with distinct patterns involving Ca{superscript 2} signalling, heat shock factors, and other biological pathways contributing to cellular homeostasis. Gene expression and lipid profiles in chia leaves responded dynamically to both short-term (3 h) and prolonged (27 h) heat stress (38{degrees}C/20{degrees}C). An almost complete return to baseline was observed, with all but 0.3% of heat-responsive genes reverting to control expression levels after 24 h. Our analysis confirms the role of Ca{superscript 2}-mediated signalling pathways and molecular chaperones, including heat shock proteins and heat shock factors, which have been previously shown to contribute to maintaining cellular function during heat stress in other plant species. Among 287 annotated lipid species, TGs exhibited the most significant and reversible changes (>2-fold), suggesting their involvement in membrane remodelling. Our findings reveal adaptive mechanisms in chia that may open avenues for enhancing thermotolerance in other heat-sensitive oilseed crops. SIGNIFICANCE STATEMENTUnderstanding how crops respond to heat stress is crucial as global temperatures rise. This study indicates that in chia (Salvia hispanica), pathways responding to heat stress, like calcium signalling and heat shock proteins, are rapidly activated, and leaf triacylglycerol levels rise under heat stress before returning to baseline during recovery. By demonstrating near-complete recovery of gene expression following heat exposure, these findings highlight mechanisms of thermotolerance that may support improved stress tolerance in other crops.

plant biology↗

bioRxiv2024

Bacterial metabarcoding reveals plant growth promoting members of the core Brachypodium distachyon root-associated microbiome overlooked by culture dependent techniques

Biofertilisers comprised of plant growth promoting bacteria (PGPB) present a promising sustainable alternative to synthetic fertilisers. Bacteria which consistently colonise roots of specific plants across distinct environments, known as that plants core root microbiome, are particularly promising due to their colonisation competency. However, traditional, culture-based techniques can overlook promising PGPB which do not display commonly screened for plant growth promoting traits. Although numerous studies have isolated beneficial root bacteria, few have combined bacterial metabarcoding with culture-based techniques to identify novel biofertiliser candidates. In a two-pronged approach, 16S rRNA amplicon sequencing was used to define the core root microbiome of the model cereal plant, Brachypodium distachyon, grown in four distinct soils. From 7,042 amplicon sequence variants (ASVs) detected in root fractions, only 40 ASVs were common at a prevalence of 80%. Core ASVs primarily belonged to the class Alphaproteobacteria, with the remainder comprising Actinobacteria, Bacilli, Chloroflexia, Gammaproteobacteria and Negativicutes. Secondly, B. distachyon root-associated bacterial strains were isolated from plants grown in the aforementioned soils. Of 207 root-associated isolates, 10 were identified as members of the core root microbiome, with the majority not displaying commonly screened for plant growth promoting traits. However, in a semi-hydroponic system, a core Bacillus and Rhodococcus strain significantly increased B. distachyon shoot dry weight by 32.8% and 40.0%, respectively. Additionally, two core Bacillus strains significantly increased root dry weight by 79.7 and 52.3%. This study demonstrates the potential of incorporating additional criteria afforded by culture-independent methods to screen for novel biofertiliser candidates typically overlooked by culture-dependent techniques. ImportanceBiofertilisers comprised of plant growth promoting bacteria (PGPB) present a sustainable, environmentally friendly alternative to synthetic fertilisers. The search for PGPB has historically relied on culture dependent methods to shortlist candidates by screening for plant growth promoting traits, such as N fixation or production of the plant hormone indole-3-acetic acid before conducting in planta trials. However, these screens may overlook promising bacterial strains which might promote plant growth via indeterminant mechanisms. Culture independent methods can take a snapshot of an entire microbiome without the need for culturing bacteria, allowing for additional selection criteria to be used when shortlisting PGPB. Our results show that targeting bacterial taxa which consistently colonise the roots of the model grass Brachypodium distachyon allowed for selection of bacterial isolates which were overlooked by culture-based PGPB trait screens. This result highlights the utility of combining traditional, culture-dependent methods with culture-independent techniques when searching for novel biofertiliser candidates.

microbiology↗

bioRxiv2023

Comparative Genomics Points to Tandem Duplications of SAD Gene Clusters as Drivers of Increased ω-3 Content in S. hispanica Seeds

O_LIA high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. C_LIO_LIAncestral whole-genome duplication events have not promoted the high -linolenic acid content in S. hispanica seeds C_LIO_LITandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high {omega}-3 content in chia seeds. C_LI Salvia hispanica L. (chia) is an abundant source of {omega}-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high -linolenic acid (ALA, {omega}-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase (ShSAD) gene family, is the main driver of the abundance of {omega}-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving {omega}-3 content in other oil crops.

genomics↗

bioRxiv2023

Leaf metabolic traits reveal hidden dimensions of plant form and function

The plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4 - a powerful framework for describing plant form and function5-7 - to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization - a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5-7, while being at least equally important to them. Our findings question classical trait6 and plant defense8 theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.

ecology↗

bioRxiv2023

Mitochondrial Complex I activity is inhibited by changes in the abundance of phosphatidylinositol and phosphatidylserine in wheat plants exposed to high temperatures.

Identifying the molecular basis of thermotolerance in crops is becoming increasingly important with the changing climatic conditions that challenge future food security. Sustaining cellular energy production under heat stress is vital in maintaining an uninterrupted growth cycle, and thus the mitochondria is instrumental in facilitating the overall heat-tolerance of a crop plant. Using targeted mass spectrometry, the changes in abundance of the lipo-protein network in mitochondrial membranes following a short episode of extremely high temperature were analysed in two wheat cultivars of differing thermotolerance. The results indicated that membrane lipids remodel in favour of shorter fatty acyl tails, and an increase in the abundance of phosphatidylinositol, while specific to the heat-tolerant cultivar was an increase in the abundance of phosphatidylserine. The differences between the lipid profiles of the two cultivars is a likely explanation for the decrease in Complex I NADH dehydrogenase activity in the heat-sensitive cultivar. Further metabolite analysis by LC-MS revealed malate accumulation, indicating that the disruption in Complex I activity impacts the catabolism of reducing equivalents. The measured increase in the total amount of phosphatidylserine in the heat-tolerant cultivar suggests a potential role in conveying thermotolerance for this minor membrane constituent, and highlights that a focus on membrane lipid composition during thermal stress will be essential for the breeding of future heat tolerant crops. SummaryO_LIWe evaluated changes to the lipo-protein network of wheat mitochondria of differing heat tolerance in response to heat shock. C_LIO_LIUsing targeted mass spectrometry, candidate transitions were selected to quantify changes in membrane lipids and the embedded protein components of the electron transport chain, which play a vital role in maintaining respiration. C_LIO_LIA significant increase in phosphatidylserine was exclusive to the mitochondria of the heat-tolerant wheat cultivar. In the absence of this, the heat-sensitive cultivar displayed a reduced Complex I activity. C_LIO_LIThe minor membrane constituent phosphatidylserine plays a role in conveying thermotolerance, making this membrane lipid a focal point for the breeding of future heat tolerant crops. C_LI

plant biology↗

bioRxiv2022

Remodelled Ribosomes Synthesise a Specific Proteome in Proliferating Plant Tissue during Cold

Plant acclimation to low temperatures occurs through system-wide mechanisms that include proteome shifts, some of which occur at the level of protein synthesis. All proteins are synthesised by ribosomes. Rather than being monolithic, transcript-to-protein translation machines, ribosomes can be selective and cause effective proteome shifts required for successful temperature acclimation. Here, we use apical root meristems of germinating seedlings of the monocotyledonous plant barley as a model to study changes in protein abundance and synthesis rates during cold acclimation. We measure metabolic and physiological parameters that allow us to compare protein synthesis rates in different physiological states, e.g., in cold acclimation compared to the optimal temperature state. We show that ribosomal proteins are independently synthesised and assembled into ribosomal complexes in root proliferative tissue, and assess how the ribo-proteome shifts during cold may be associated with changes in synthesis and accumulation of macromolecular complexes. We demonstrate that translation initiation is the limiting step during cold acclimation and based on our data propose a model of a ribosomal code that depends on a reconfigured ribosome population, where as a mode of cold acclimation, specific ribosomal protein compositions may confer selective association capabilities between 60S subunits and 48S initiation complexes.

plant biology↗

bioRxiv2021

Low doses of the organic insecticide spinosad trigger lysosomal defects, ROS driven lipid dysregulation and neurodegeneration in flies

The plight of insect populations around the world and the threats it poses to agriculture and ecosystems has thrown insecticide use into the spotlight. Spinosad is an organic insecticide, considered less harmful to beneficial insects than synthetic insecticides, but its mode of action remains unclear. Using Drosophila, we show that low doses of spinosad reduce cholinergic response in neurons by antagonizing D6 nAChRs. D6 nAChRs are transported to lysosomes that become enlarged and accumulate upon spinosad treatment. Oxidative stress is initiated in the central nervous system, and spreads to midgut and disturbs lipid storage in metabolic tissues in a D6-dependent manner. Spinosad toxicity was ameliorated with the antioxidant N-Acetylcysteine amide (NACA). Chronic exposures lead to mitochondrial defects, severe neurodegeneration and blindness in adult animals. The many deleterious effects of low doses of this insecticide reported here point to an urgent need for rigorous investigation of its impacts on beneficial insects.

neuroscience↗

bioRxiv2020

Investigation of biochemical changes in barley inoculated with Trichoderma harzianum T-22 under salt stress

Increases in soil salinity impacts growth and yield of agricultural plants by inhibiting plant functions. Soil salinization is increasing because of the pressure of a growing population on food supply. Genetically modified crops and plant breeding techniques are being used to produce plants tolerant to salt stress. However, interactions of fungal endophytes with crop plants can also improve tolerance and is a less expensive approach. Here, the role of Trichoderma harzianum T-22 in alleviating NaCl-induced stress in two barley genotypes (cv. Vlamingh and cv. Gairdner) has been investigated. Metabolomics using GC-MS for polar metabolites and LC-MS for lipids was employed to provide insights into the biochemical changes in barley roots inoculated with fungus during the early stages of interaction. T. harzianum increased the root length of both genotypes under controlled and saline conditions. The fungus reduced the relative concentration of sugars in both genotypes and caused no change in organic acids under saline conditions. Amino acids decreased only in cv. Gairdner in fungus-inoculated roots under saline conditions. Lipid analyses suggest that salt stress causes large changes in the lipid profile of roots but that inoculation with fungus greatly reduces the extent of these changes. By studying a tolerant and a sensitive genotype and their responses to salt and inoculation we have been able to develop hypotheses about what lipid species and metabolites may be involved in the tolerant genotype for its tolerance to salt and how fungal inoculation changes the response of the sensitive genotype to improve its tolerance.

biochemistry↗

bioRxiv2020

Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation

Arabidopsis REIL proteins are cytosolic ribosomal 60S-biogenesis factors. After shift to 10{degrees}C, reil mutants deplete and slowly replenish non-translating eukaryotic ribosome complexes of root tissue, while tightly controlling the balance of non-translating 40S- and 60S-subunits. Reil mutations compensate by hyper-accumulation of non-translating subunits at steady-state temperature; after cold-shift, a KCl-sensitive 80S sub-fraction remains depleted. We infer that Arabidopsis buffers fluctuating translation by pre-existing non-translating ribosomes before de novo synthesis meets temperature-induced demands. Reil1 reil2 double mutants accumulate 43S-preinitiation and pre-60S-maturation complexes and have altered paralog composition of ribosomal proteins in non-translating complexes. With few exceptions, e.g. RPL3B and RPL24C, these changes are not under transcriptional control. Our study suggests requirement of de novo synthesis of eukaryotic ribosomes for long-term cold acclimation, feedback control of NUC2 and eIF3C2 transcription and links new proteins, AT1G03250, AT5G60530, to plant ribosome biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for cold acclimation. Highlight of this studyREIL proteins affect paralog composition of eukaryotic ribosomes and suppress accumulation of 43S-preinitiation and pre-60S-maturation complexes, suggesting functions of ribosome heterogeneity and biogenesis in plant cold acclimation.

plant biology↗

bioRxiv2019

Integrative Multi-Omics Analysis of Barley Genotypes Shows Differential Salt-Induced Osmotic Barriers and Response Phases Among Rootzones

The mechanisms underlying rootzone-localised responses to salinity stress during early stage of barley development remains fragmentary and elusive. Here, we performed a comprehensive detection of the multi-root-omes (transcriptomes, metabolomes, lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) with seedling root growth maintained and restricted in response to salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEG) or abundant metabolites (DAM) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, maturation Z3). Based on pathway over-representation of the DEG and DAM, phenylpropanoid biosynthesis is the most statistically over-represented biological pathways among all salinity responses observed. Together with the histological evidence, an intense salt-induced lignin impregnation was found only at the stelic cell wall of Clipper Z2, comparing to a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on global correlation network construction of the DEG and DAM, callose deposition that potentially adjusted the symplastic flow in roots was almost independent of salinity in rootzones of Clipper, but was markedly decreased in that of Sahara. Through closer examinations of molecular and hormonal clues, we further demonstrate that the salinity response in rootzones of Clipper were mostly at recovery phase, comparing to Sahara with rootzones retained at quiescence. Taken together, we propose that two distinctive salt tolerance mechanisms could exist in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with the deteriorating global salinization of soil.

plant biology↗

bioRxiv2018

Phenotypic plasticity facilitates alterations in life-history strategies under combinations of environmental stresses

Plants developed various reversible and non-reversible acclimation mechanisms to cope with the multifaceted nature of abiotic stress combinations. We hypothesized that in order to endure these stress combinations, plants elicit distinctive acclimation strategies through specific trade-offs between reproduction and defense. To investigate Brachypodium distachyon acclimation strategies to combinations of salinity, drought and heat, we applied a system biology approach, integrating physiological, metabolic and transcriptional analyses. We analyzed the trade-offs among functional and performance traits, and their effects on plant fitness. A combination of drought and heat resulted in escape strategy, while under a combination of salinity and heat, plants exhibited avoidance strategy. On the other hand, under combinations of salinity and drought, with or without heat stress, plant fitness (i.e. germination rate of subsequent generation) was severely impaired. These results indicate that under combined stresses, plants life-history strategies were shaped by the limits of phenotypic and metabolic plasticity and the trade-offs between traits, thereby giving raise to distinct acclimations. Our findings provide a mechanistic understanding of plant acclimations to combinations of abiotic stresses and shed light on the different life-history strategies that can contribute to grass fitness and possibly to their dispersion under changing environments.

plant biology↗

bioRxiv2017

Best Practice Data Life Cycle Approaches for the Life Sciences

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a life cycle view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain.\n\nHere we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on omics datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

bioinformatics↗