Biology subjects

Seybold, H.

Publications and source records attributed to Seybold, H..

5 recordsLinked to original sources

bioRxiv2026

Large river eDNA sampling designs with remote-sensing-based clustering stratification

Environmental DNA (eDNA) provides a powerful tool for biodiversity monitoring in large river ecosystems. However, current studies often rely on subjective site selection and lack systematic sampling designs. This can limit the ability to capture the full spectrum of environmental conditions that species depend on, thereby compromising sampling efficiency. To address this challenge, we propose utilizing remote sensing-based clustering for environmental stratification of sampling designs, thereby enhancing detection capabilities and increasing the objectivity of eDNA sampling. Using GBIF-based fish species distribution models and simulated distributions along the Danube, we demonstrate that this approach enhances detection efficiency compared to conventional random and regular sampling methods. To facilitate practical implementation, we developed a tool to help fieldwork planners of river sampling campaigns automatically apply this method and select stratified sampling sites without the need for extensive data processing. Finally, we demonstrate that eDNA detection occurred most frequently within the range of 0-20km downstream of the expected modeled distribution of species, suggesting that the diffusion of the signal should be further considered in the sampling design process. Our findings highlight the potential of remote sensing-based stratification to create more efficient and objective sampling designs but suggest that sampling design should be further combined with hydrological information to optimize cost-efficient sampling. The development of standard and robust sampling protocols will help advance more cost-effective eDNA-based biodiversity monitoring in riverine ecosystems.

ecology↗

bioRxiv2024

Autophagy at Crossroads: Modulating Responses to Combined Stresses, Unveiling Metabolic Shifts and Bacterial Dependencies

Plants face diverse stresses in natural environments, necessitating complex responses for survival. Abiotic and biotic stress responses are typically counteractive, posing challenges for breeding crops resilient to multiple stresses. Autophagy, a cellular transport process, plays a vital role in plant stress response, facilitating the degradation of cellular components and enabling nutrient recycling. Here, we asked what the role of autophagy is in combined abiotic (heat) and biotic (bacterial infection by Xanthomonas campestris pv. vesicatoria) stress. We introduce a conceptual framework based on assays monitoring autophagy activation, bacterial infection, and metabolic profiling. We observed that heat stress facilitates bacterial growth in an autophagy-dependent manner. Bacterial effectors facilitate this phenomenon. We also demonstrate the engagement of the autophagy-related 8 (ATG8) protein family members in stress-specific activation. Metabolic profiling highlights effector-dependent shifts in nutrient availability during stress, influencing bacterial performance. Our study challenges the assumption that combined stresses are simply the sum of individual responses as exemplified by activation of the autophagic pathway. Instead, it establishes autophagy as a link connecting environmental factors and plant-microbe interactions. Insights for our study can present a novel perspective for designing strategies to enhance crop resilience in the face of multifaceted challenges.

plant biology↗

bioRxiv2019

Prioritization of abiotic and biotic stress responses by direct linkage of ABI1 phosphatase and CPK5 calcium-dependent protein kinase

In nature plants are constantly challenged by simultaneous abiotic and biotic stresses, and under conflicting stress scenarios prioritization of stress responses is required for plant survival. Calcium-dependent protein kinase CPK5 is a central hub in local and distal immune signaling, required for hormone salicylic acid (SA)-dependent immunity and pathogen resistance. Here we show that CPK5-dependent immune responses and pathogen resistance are inhibited upon abscisic acid (ABA) treatment or in genetic mutant backgrounds lacking PP2C phosphatase activities including abi1-2, whereas immune responses are enhanced by co-expression of active ABI1 phosphatase variants. Biochemical studies and mass spectrometry-based phospho-site analysis reveal a direct ABI1 phosphatase-catalyzed de-phosphorylation of CPK5 auto-phosphorylation site T98. Mimicking continuous de-phosphorylation in CPK5T98A leads to enhanced ROS production and more resistant plants, mimicking the auto-phosphorylated status in CPK5T98D, reduces CPK5-mediated immune responses. Mechanistic insight identifies differential phosphorylation at T98 in the N-terminal domain of CPK5 to control the level of interaction between the kinase and its substrate protein rather than CPK5 catalytic activity. Thus, CPK5-catalyzed immune signaling may become discontinued even at an elevated cytoplasmic calcium concentration. Our work reveals an elegant mechanism for stress response prioritization in plants: The ABA-dependent phosphatase ABI1, negative regulator of abiotic responses, functions as positive regulator of biotic stress responses, stabilizing CPK5-dependent immune signaling in the absence of ABA. Continuous pathogen survey activates plant immunity in environmentally friendly conditions, whereas under severe abiotic stress the phosphatase/kinase pair prohibits immune signaling through a direct biochemical switch involving two key regulatory enzymes of these antagonistic pathways. Significance StatementPlants challenged by simultaneous abiotic and biotic stresses must prioritize in conflicting scenarios to guarantee survival. Pathogen resistance and immune memory depends on the phytohormone salicylic acid (SA). Adaptation to abiotic stress signaling involves the phytohormone abscisic acid (ABA). We identify a direct biochemical switch by which ABA-mediated abiotic signaling prioritizes over SA-dependent immune responses via reversible phosphorylation at a single protein mark involving two key regulatory enzymes of these antagonistic pathways. Phosphatase ABI1 de-phosphorylates calcium-dependent protein kinase CPK5 at an auto-phosphorylation site T98, which effects the interaction efficiency between the kinase and its substrate. Under abiotic stress ABA mediates phosphatase inhibition, which facilitates prolonged auto-phosphorylation of CPK5, preventing CPK5 substrate interaction and ultimately stop CPK5-mediated immune signaling.

plant biology↗

bioRxiv2019

Hemibiotrophic fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition

Yield losses caused by fungal pathogens represent a major threat to global food production. One of the most devastating fungal wheat pathogens is Zymoseptoria tritici. Despite the importance of this fungus and wheat as main staple food crop the underlying mechanisms of plant-pathogen interactions are poorly understood. Here we present a conceptual framework based on coinfection assays, comparative metabolomics, and microbiome profiling to study the interaction of Z. tritici in susceptible and resistant wheat. We demonstrate that Z. tritici suppresses the production of immune-related metabolites in a susceptible cultivar. Remarkably, this fungus-induced immune suppression spreads within the leaf and even to other leaves, a previously undescribed phenomenon that we term \"systemic induced susceptibility\". Using a comparative metabolomics approach, we identified defense-related biosynthetic pathways that are suppressed and induced in susceptible and resistant cultivars, respectively. We show that these fungus-induced changes also dramatically affect the wheat leaf microbiome. Our findings emphasize that immune suppression by this hemibiotrophic pathogen impacts specialized plant metabolism, alters its associated microbial communities, and renders wheat vulnerable to further infections.

plant biology↗

bioRxiv2017

Extremely flexible infection programs in a fungal plant pathogen

Filamentous plant pathogens exhibit extraordinary levels of genomic variability that is proposed to facilitate rapid adaptation to changing host environments. However, the impact of genomic variation on phenotypic differentiation in pathogen populations is largely unknown. Here, we address the extent of variability in infection phenotypes of the hemibiotrophic wheat pathogen Zymoseptoria tritici by studying three field isolates collected in Denmark, Iran, and the Netherlands. These three isolates differ extensively in genome structure and gene content, but produce similar disease symptoms in the same susceptible wheat cultivar. Using advanced confocal microscopy, staining of reactive oxygen species, and comparative analyses of infection stage-specific RNA-seq data, we demonstrate considerable variation in the temporal and spatial course of infection of the three isolates. Based on microscopic observation, we determined four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction. Comparative analyses of the fungal transcriptomes, sequenced for every infection stage, revealed that the gene expression profiles of the isolates differed significantly, and 20% of the genes are differentially expressed between the three isolates during infection. The genes exhibiting isolate-specific expression patterns are enriched in genes encoding effector candidates that are small, secreted, cysteine-rich proteins and putative virulence determinants. Moreover, the differentially expressed genes were located significantly closer to transposable elements, which are enriched for the heterochromatin-associated histone marks H3K9me3 and H3K27me3 on the accessory chromosomes. This observation indicates that transposable elements and epigenetic regulation contribute to the infection-associated transcriptional variation between the isolates. Our findings illustrate how high genetic diversity in a pathogen population can result in highly differentiated infection and expression phenotypes that can support rapid adaptation in changing environments. Furthermore, our study reveals an exceptionally high extent of plasticity in the infection program of an important wheat pathogen and shows a substantial redundancy in infection-related gene expression.\n\nAuthor summaryZymoseptoria tritici is a pathogen that infects wheat and induces necrosis in leaf tissue. Z. tritici field populations exhibit high levels of genetic diversity, and here we addressed the consequences of this diversity on infection phenotypes. We conducted a detailed comparison of the infection processes of three Z. tritici isolates collected in Denmark, the Netherlands, and Iran. We inoculated leaves of a susceptible wheat cultivar and monitored development of disease symptoms and infection structures in leaf tissue by confocal microscopy. The three isolates exhibited highly differentiated spatial and temporal patterns of infection, although quantitative disease was similar. Furthermore, more than 20% of the genes were differentially expressed in the three isolates during wheat infection. Variation in gene expression is particularly associated with transposable elements, suggesting a role of epigenetic regulation in transcriptional variation among the three isolates. Finally, we find that genes encoding putative virulence determinants were enriched among the differentially expressed genes, suggesting that each of the three Z. tritici isolates utilizes different strategies to manipulate host defenses. Our results emphasize that phenotypic diversity plays an important role in pathogen populations and should be considered when developing crop protection strategies.

plant biology↗