Biology subjects

Schiessl, K.

Publications and source records attributed to Schiessl, K..

8 recordsLinked to original sources

bioRxiv2026

4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs

Legume root nodules enable symbiotic nitrogen fixation through the development of specialized cells that accommodate nitrogen-fixing bacteria intracellularly and support bacterial nitrogenase activity. Here, we present a 4D (3D space and time) spatial transcriptomic atlas of Medicago truncatula nodules and lateral roots, revealing specialized symbiotic cell types that develop alongside a conserved lateral-root-derived program that underpins vascularization. Spatial profiling of both plant and bacterial transcripts resolves distinct transcriptional states and previously unrecognized cell states. Spatial analysis of developmental regulator mutants uncovers a cascading series of cell-type-specific programs during nodule maturation. LSH1/LSH2 are central regulators of these programs, and lsh1/lsh2 mutants exhibit collapse of hormonal gradients and nodule identity. Strikingly, loss of nodule identity collapses to a primary-root identity rather than lateral-root fate. This work reveals how tissue complexity emerges through stacked developmental programs sustained in distinct cellular compartments, allowing the emergence of cell types specialized for harboring nitrogen-fixing bacteria. HIGHLIGHTSO_LI>136,000 cells define a 4D spatial atlas of nodules and lateral roots C_LIO_LI3D spatial and dual-species analysis resolves dynamic host and rhizobial cell states C_LIO_LIA shared meristem generates 3 spatially coordinated symbiotic, non-symbiotic, and vascular cell programs C_LIO_LILSH1/LSH2 are critical for regulatory programs underlying nodule development and identity C_LIO_LINodule identity loss collapses toward a primary root-associated state, not a lateral root fate C_LI

plant biology↗

bioRxiv2025

A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors

In industrial biotechnology, cell density is a critical parameter that influences key process control variables such as feed rate, harvest timing, and product recovery. Traditional biomass measurements are indirect, incapable of quantifying population heterogeneity, and often prone to inaccuracies due to manual handling and interference from culture media compounds. This study introduces an automated flow cytometry approach to enable continuous, real-time monitoring of bacterial cultures in a continuous bioreactor. Our method employs a double-staining protocol that combines DAPI for assessing total DNA content with Alexa Fluor 488 via Click-iT technology to detect the percentage of cells with active DNA replication through EdU incorporation. This streamlined protocol, which integrates cell fixation, permeabilization, staining, and measurement, was applied to three Gram-negative strains: Bradyrhizobium sp., Escherichia coli, and Stenotrophomonas rhizophila. The approach successfully captured both growth dynamics and cell cycle progression, providing rapid and quantitative insights into culture composition. The enhanced temporal resolution achieved by this method facilitates timely adjustments of process parameters, ultimately improving bioprocess efficiency and product quality. These results underscore the potential of automated flow cytometry as a powerful tool for real-time monitoring and control in industrial biotechnology.

microbiology↗

bioRxiv2023

Cellular gibberellin dynamics govern indeterminate nodule development, morphologyand function

During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determined the cellular location and function of bioactive GA during nodule organogenesis using a genetically-encoded second generation GA biosensor, GPS2. We found endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions and maintaining accumulation in the mature nodule meristem. We show, through mis-expression of GA catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that cytokinin as well as nodule-identity genes induce and sustain GA accumulation necessary for nodule function.

plant biology↗

bioRxiv2023

Light sensitive short hypocotyl (LSH) confer symbiotic nodule identity in the legume Medicago truncatula

Legumes grow specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting beneficial nitrogen-fixing bacteria that provide the plant with a nitrogen source. We have previously shown that a lateral root-like program underpins nodule initiation, but there must be additional developmental programs that confer nodule identity. Here, we show that two members of the LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define organ boundaries and meristem complexity in the shoot, function as regulators of nodule organ identity. LSH1/LSH2 function upstream of and together with the known nodule regulators Nuclear Factor Y-A1 and NODULE ROOT1/2. The principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, the unique nodule feature. We conclude that the coordinate recruitment of a pre-existing primordium identity program, in parallel to a root initiation program, underpins the divergence between lateral roots and nodules.

plant biology↗

bioRxiv2022

The peptide GOLVEN10 controls nodule and lateral root organogenesis and positioning along the longitudinal root axis

O_LIGLV/RGF peptide encoding genes can be identified in genomes of all plants that can form roots or root-like structures suggesting they were essential for transition of plants to land. C_LIO_LIIn Medicago truncatula, five of fifteen GOLVEN(GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide coding genes were induced during nodule organogenesis and to a varying extent under nitrogen deficiency and auxin treatment. Expression of MtGLV9 and MtGLV10 at nodule initiation sites was dependent on the transcription factor NODULE INCEPTION. C_LIO_LIOverexpression of all five nodule-induced GLV genes in M. truncatula hairy roots as well as application of the corresponding synthetic peptides resulted in a 25-50% reduction in nodule number indicating GOLVENs are negative regulators of nodule organogenesis. C_LIO_LIThe peptide GOLVEN10 shifted the position of the first formed lateral root (rhizotaxis) as well as the first formed nodule along the longitudinal primary root axis, a phenomenon we term nodulotaxis, thereby reducing the absolute length of the zone of lateral organ formation on roots. C_LIO_LIApplication of synthetic GOLVEN10 peptide caused an increase in cell number but not cell length in each root cortical cell layer causing an increase in root length and a consequent spatiotemporal delay in formation of the first lateral organ. C_LI Plain Language SummaryNodule positioning is an understudied trait, yet it determines the length of the root that can support nodule formation and consequently the total number of functional nodules formed. We identify for the first time, genetic factors called GOLVEN peptides that alter nodule and lateral root positioning on the primary root along with several other traits including nodule organ initiation and root architecture.

plant biology↗

bioRxiv2016

Benefits of siderophore release lie in mediating diffusion limitation at low iron solubility

Siderophores are chelators released by many bacteria to take up iron. In contrast to iron receptors located at the cell surface, released siderophores are at risk of being lost to environmental sinks. Here, we asked the question whether the release itself is essential for the function of siderophores, which could explain why such a risky strategy is widespread. We developed a reaction-diffusion model to determine the impact of siderophore release on overcoming iron limitation caused by poor solubility in aerobic, pH-neutral environments. We found that secretion of siderophores can efficiently accelerate iron uptake at low solubility, since secreted siderophores solubilize slowly diffusing large iron aggregates to small, quickly diffusing iron-siderophore complexes. At high iron solubility, however, when the iron-siderophore complex is no longer considerably smaller than the iron source itself, siderophore secretion can also slow down iron uptake. In addition, we found that cells can synergistically share their siderophores, depending on their distance and the level of iron aggregation. Overall, our study helps understand why siderophore secretion is so widespread: Even though a large fraction of secreted siderophores is lost, the solubilization of iron through secreted siderophores can efficiently increase iron uptake, especially if siderophores are produced cooperatively by several cells.

microbiology↗

bioRxiv2016

Individual- versus group-optimality in the production of secreted bacterial compounds

How unicellular organisms optimize the production of compounds is a fundamental biological question. While it is typically thought that production is optimized at the individual-cell level, secreted compounds could also allow for optimization at the group level, leading to a division of labor where a subset of cells produces and shares the compound with everyone. Using mathematical modelling, we show that the evolution of such division of labor depends on the cost function of compound production. Specifically, for any trait with saturating benefits, linear costs promote the evolution of uniform production levels across cells. Conversely, production costs that diminish with higher output levels favor the evolution of specialization - especially when compound shareability is high. When experimentally testing these predictions with pyoverdine, a secreted iron-scavenging compound produced by Pseudomonas aeruginosa, we found linear costs and, consistent with our model, detected uniform pyoverdine production levels across cells. We conclude that for shared compounds with saturating benefits, the evolution of division of labor is facilitated by a diminishing cost function. More generally, we note that shifts in the level of selection from individuals to groups do not solely require cooperation, but critically depend on mechanistic factors, including the distribution of compound synthesis costs.

evolutionary biology↗

bioRxiv2016

Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

Whether microbial interactions are predominantly cooperative or competitive is a central question in microbial ecology, and determines the composition and stability of microbial communities. The secretion of iron chelators called siderophores is a model system for cooperative interactions, even though these chelators can also mediate competition by depriving competitors of iron. Using a genetically engineered experimental system based on the Pseudomonas aeruginosa siderophore pyochelin, we found that secreting siderophores to inhibit a competitor can lead to higher benefits than secreting siderophores to make iron available. Based on thermodynamic modeling, we propose that competitive inhibition by siderophores is efficient in kinetically controlled saturated systems, where dissolution of precipitated iron phases is slow. Under these conditions, met in many natural environments, secreted siderophores temporarily reduce the concentration of available iron and can thus induce growth inhibition in a competing strain, even at high iron concentrations. These findings give insight into the function of siderophores: In addition to its cooperative nature, siderophore secretion could also be a widespread mechanism for mediating competitive interactions. Our functional investigation reveals a complexity in microbial interaction networks that would remain hidden when focusing on genomic information alone.

microbiology↗