Biology subjects

Neuhauser, S.

Publications and source records attributed to Neuhauser, S..

13 recordsLinked to original sources

bioRxiv2025

Under the cover of darkness: how clubroot disease affects Arabidopsis thaliana physiology during the night

Plasmodiophora brassicae (Phytomyxea, Rhizaria) is the etiological agent of clubroot disease, one of the most important diseases of Brassicaceae crops. Alteration of metabolism and hormone homeostasis leads to the formation of tumour-like galls in the roots of affected plants. Host plant energy metabolism, defence and developmental processes are under strong temporal control and the very same processes are affected by clubroot. For the first time, this study uses time-resolved transcriptome analyses to explore how P. brassicae affects Arabidopsis thaliana in the night during intermediate (14 days after inoculation; DAI) and late (21 DAI) infection. Day-night differences in gene expression were more pronounced in younger rather than older plants in our differential gene expression (DGE) analysis. Consequently, intermediate phases of infection showed more day-night differences than later ones. Clustering of differentially expressed genes (DEGs) in functional categories highlighted how some of the typical processes known to be disrupted by clubroot infection are more significantly affected in the night and also uncovered some disrupted exclusively in the night. RNA modification stood out as the most unambiguously upregulated process in infected Arabidopsis roots in the night. Analysis of the interaction between clubroot infection and diel oscillations in gene expression detected modifications in the rhythmicity of central circadian clock components during the infection. We discuss our findings in the context of manipulation of plant defence and metabolism, identifying targets for experimental validation and highlighting potential new lines of investigation of our time-resolved datasets to better understand the interaction between P. brassicae and its host. Significance statementPlasmodiophora brassicae impacts physiological processes under strong temporal control in Brassicaceae hosts: e.g., metabolism, hormone homeostasis and defence. Here, for the first time, we performed a time-resolved transcriptomic exploration of clubroot disease at intermediate and mature stages of infection. We identify a previously unrecognised role for nocturnal manipulation of organellar RNA editing and disruption of rhythmicity in circadian clock components. We provide a dataset enabling further exploration of the impact of clubroot on plant circadian processes.

plant biology↗

bioRxiv2023

Local endoreduplication of the host is a conserved process during Phytomyxea-host interaction

Endoreduplication is a modified cell cycle in which cells duplicate their DNA without subsequent mitosis. This process is common in plants and can also be found in other organisms like algae and animals. Biotrophic plant pathogens have been shown to induce endoreduplication in their host to gain space and/or nutrients. Phytomyxea (divided into the Plasmodiophorida, the Phagomyxida, and the Marinomyxa clade) are obligate biotrophic parasites of plants, diatoms, brown algae, and oomycetes. Here, we tested if phytomyxids induce local endoreduplication in two distant hosts (plants and brown algae). By combining fluorescent in situ hybridisation (FISH) coupled with nuclear area measurements and flow cytometry, we confirmed that endoreduplication is induced by Plasmodiophora brassicae (Plasmodiophorida) in infected plants and demonstrate this process in combination with Maullinia ectocarpii and Maullinia braseltonii (Phagomyxida) in brown algae. We identified molecular signatures of endoreduplication in RNA-seq datasets of P. brassicae-infected Brassica oleraceae and M. ectocarpii-infected Ectocarpus siliculosus. Cell cycle switch proteins (CCS52A1 and B in plants and CCS52 in algae) as well as the protein kinase WEE1 (in plants) were identified as genes potentially important for the phytomyxean-induced switch from the mitotic cell cycle to the endocycle. Their expression pattern changed in infected plants and brown algae accordingly. In this study we expand the knowledge on Phytomyxea-host interactions by showing that induced endoreduplication in the host is a conserved feature in phytomyxid infections. The induction of this cellular mechanism by phytomyxid parasites in phylogenetically distant hosts further points at a fundamental importance of endoreduplication in these biotrophic interactions.

microbiology↗

bioRxiv2022

Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans

The basidiomycete Serpula lacrymans is responsible for timber destruction in houses. Basidiomycetes are known to harbor a diverse but poorly understood microbial community of bacteria, archaea, yeasts, and filamentous fungi in their fruiting bodies. In this study, we used amplicon-sequencing to analyze the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the background community structure. Our findings indicate that bacterial genera cluster depended on sample type, and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota, and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground scree. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and life style. Highlights- The prokaryote communities associated with S. lacrymans mycelia and fruiting bodies as well as wood and non-woody substrate form distinct clusters. - Across all samples 30% of OTUs were shared (core microbiome) while the number of unique OTUs was small. - Fruiting bodies (n= 8) of S. lacrymans shared a core set of 365 OTUs, dominated by Actinobacteriodota (44%), Pseudomonadota (28%), and Acidobacteriodota (9%). - Tissue/sample type is the main factor influencing diversity, followed by sample origin.

microbiology↗

bioRxiv2022

Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria)

Phagocytosis is a complex multi-gene trait of eukaryotes and allegedly one of the very defining features of this group. Although well documented for free-living unicellular eukaryotes and in specific cellular types of animals, data on phagocytosis in intracellular biotrophic parasites are scant. Indeed, the definition of intracellular biotrophy as complete reliance of a parasite on a living host, with which it constantly negotiates for the exchange of nutrients, is at odd with the consumption of particulate matter suggested by phagocytosis. Phytomyxea are intracellular biotrophic parasites infecting a broad group of hosts, ranging from plants to stramenopiles. They belong to the clade Rhizaria, where phagotrophy (i.e., phagocytosis as main mode to acquire nutrients) is the main mode of nutrition. The exact mode of nutrition of the biotrophic phytomyxea, including the agriculturally impactful phytomyxid Plasmodiophora brassicae, is still unresolved; despite investigations and the availability of molecular data. For other Phytomyxea, observations are patchy and molecular data altogether lacking. Here, using available genomic and transcriptomic data for Phytomyxea and the de novo sequenced transcriptome of the brown algae parasite Maullinia ectocarpii, we investigate the likelihood that the genetic machinery underpinning phagotrophy is conserved within the clade. We further document intracellular phagocytosis in P. brassicae and M. ectocarpii by transmission electron microscopy and fluorescent in situ hybridization. Our investigations confirm that molecular signatures underpinning phagocytosis exist in Phytomyxea and hint at a smaller subset of genes used for intracellular phagocytosis, which is similar between the two parasites. Microscopic evidence confirms the existence of intracellular phagocytosis, which seems to coexist with the manipulation of host physiology typical of biotrophic interactions. In both phytomyxid parasites investigated intracellular phagocytosis has adapted to the intracellular environment and seemingly targets specific organelles. Our findings shed light on the feeding behaviour of Phytomyxea, providing new molecular data for the class; and suggest a paramount and previously unrecognised role for phagocytosis in biotrophic interactions between host and parasite.

microbiology↗

bioRxiv2022

Unveiling hidden eukaryotes: diversity of Endomyxa (Rhizaria) in coastal marine habitats

Nucleic acid based studies of marine biodiversity often focus on Kingdom-level diversity. Such approaches often largely miss diversity of less studied groups, likely to harbour many unknown lineages which are likely playing significant ecological roles. Among these elusive groups are Endomyxa (Rhizaria), a ubiquitous, but understudied lineage comprising parasites (e.g. Ascetosporea, Phytomyxea), free-living amoebae (e.g. Vampyrellida, Gromia, Filoreta), flagellates (e.g. Tremula, Aquavolon), and unknown environmental lineages. Using Endomyxa-biased primers targeting the hypervariable region V4 of the 18S rRNA gene, we explored the diversity of Endomyxa in marine samples from European coastal sites and compared it to that found in pan-eukaryote V4 libraries of the same samples. In total 458 endomyxan OTUs were identified, of which 38% were only detected by the specific primers. Most are distinct from published sequences, and include novel diversity within known clades, and putative novel lineages. The data revealed variations in endomyxan assemblages related to habitat (benthic vs. pelagic, sampling site), mode of nutrition (parasitic vs. free-living) and nucleic acid type (DNA vs. RNA). Overall, the vast majority of endomyxan diversity occurs in sediments (including Vampyrellida, Reticulosida, and the environmental "Novel Clade 12") where they form diverse and active communities including many uncharacterised lineages.

microbiology↗

bioRxiv2022

The global distribution and environmental drivers of the soil antibiotic resistome

BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earths largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents, and created the first global atlas with the distributions of topsoil ARGs. ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.

ecology↗

bioRxiv2021

PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery

We created the PDX Network (PDXNet) Portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources (i.e., PDX models, sequencing data, treatment response data, and bioinformatics workflows), to facilitate collaboration among researchers, and to make resources easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols, and training materials for processing PDX data. The initial portal release highlights PDXNet model and data resources, including 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCIs Patient-Derived Model Repository (PDMR) for public access. These models have 2,822 associated sequencing files from 873 samples across 307 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal also includes results from standardized analysis workflows on PDXNet sequencing files and PDMR data (2,594 samples from 463 patients across 78 disease types). These 15 analysis workflows for whole-exome and RNA-Seq data are freely available, robust, validated, and standardized. The model and data lists will grow substantially over the next two years and will be continuously updated as new data are available. PDXNet models support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials. The PDXNet portal is a centralized location for these data and resources, which we expect to be of significant utility for the cancer research community.

cancer biology↗

bioRxiv2020

Bacterial community associated with the dry-rot fungus Serpula lacrymans is dominated by Firmicutes and Proteobacteria

The dry-rot fungus Serpula lacrymans causes enormous structural damage by decaying construction timber thereby resulting in tremendous financial loss. Dry-rot fungi decompose cellulose and hemicellulose and, if the wood remains wet, are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions have considerable impact on all interaction partners ranging from antagonistic to beneficial relationships. However, little is known about possible interaction partners of S. lacrymans. Here we show that S. lacrymans has many co-existing, mainly Gram-positive bacteria. By investigating differences in the bacterial community associated with fruiting bodies, mycelia and rhizomorphs, we provide evidence of preferential colonization of S. lacrymans tissues by certain bacterial phyla. Bacteria isolated from fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were found in lower abundances. In situ fluorescence hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells, sometimes also attached to fungal spores. In co-culture, single bacterial isolates caused growth inhibition of S. lacrymans and vice versa. Additionally, certain bacteria induced pigment production in the fungus. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria are able to influence the behavior, e.g. growth and secondary metabolite production, of S. lacrymans in culture. ImportanceSerpula lacrymans is a very effective dry-rot causing fungus, specialized in degradation of coniferous timber in houses. The initial colonization is favored by water damage, and after establishment, the fungus starts to destruct cellulose and hemicellulose. It is among the most feared wood-rotting fungi in the built environment as the remediation of S. lacrymans damaged buildings is expensive and tedious. After improper renovation, the possibility of a recolonization by S. lacrymans is likely. As bacteria influence fungal establishment on wood, the need to investigate the bacterial community associated with S. lacrymans is apparent. The significance of our research is in identifying and characterizing bacteria associated with S. lacrymans. This will allow the assessment of their influence on fungal life style, leading to a broader understanding of the properties that make S. lacrymans so extraordinarily aggressive at decaying wood compared to other indoor wood destroyers.

ecology↗

bioRxiv2020

Dynamic cell wall modifications in brassicas during clubroot disease

Biotic interactions of plants and microbial pathogens can cause drastic changes in cell wall composition in response to developmental reprogramming caused as consequence of an infection. Clubroot disease, caused by the biotrophic plant pathogen Plasmodiophora brassicae (Phytomyxea, Rhizaria), is the economically most important disease of Brassica crops worldwide. The disease is best known by the characteristic hypertrophied roots (root galls, clubroots). Amongst a series of physiological changes of the host tissue, the formation of the characteristic root galls leads to cell wall modification and reorganization. Cell wall chemistry and the hosts genetic repertoire are discussed to play a role in the resilience of plants against clubroot disease. Plant cells infected with P. brassicae are markedly enlarged, and look very differently from uninfected, healthy cells. Here we systematically review cell wall related processes that lead to the typical clubroot phenotype and provide novel insights how P. brassicae uses these modifications to benefit its own development. An infection with P. brassicae impacts on nearly all cell wall related processes, but all alterations are meaningful for successful growth and development of P. brassicae. Processes related to cell wall stability and rigidity (e.g. cellulose, pectin or lignin synthesis) are down-regulated, while cell wall degrading enzymes or processes that increase the flexibility of the host cell wall (e.g. expansin) are up-regulated. The here presented findings indicate that P. brassicae weakens the structural stability of its host cell while it increases its elasticity, which in consequence allows P. brassicae to grow bigger and ultimately to develop more resting spores. Consequently, the understanding of the modification of the host cell wall is important for the formation of the characteristic root galls but also to better understand clubroot disease.

plant biology↗

bioRxiv2019

Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis

Patient-Derived Xenografts (PDXs) are tumor-in-mouse models for cancer. PDX collections, such as those supported by the NCI PDXNet program, are powerful resources for preclinical therapeutic testing. However, variations in experimental design and analysis procedures have limited interpretability. To determine the robustness of PDX studies, the PDXNet tested temozolomide drug response for three pre-validated PDX models (sensitive, resistant, and intermediate) across four blinded PDX Development and Trial Centers (PDTCs) using independently selected SOPs. Each PDTC was able to correctly identify the sensitive, resistant, and intermediate models, and statistical evaluations were concordant across all groups. We also developed and benchmarked optimized PDX informatics pipelines, and these yielded robust assessments across xenograft biological replicates. These studies show that PDX drug responses and sequence results are reproducible across diverse experimental protocols. Here we share the range of experimental procedures that maintained robustness, as well as standardized cloud-based workflows for PDX exome-seq and RNA-Seq analysis and for evaluating growth.

cancer biology↗

bioRxiv2018

Transcriptomic response in symptomless roots of clubroot infected kohlrabi mirrors resistant plants

BackgroundClubroot disease caused by Plasmodiophora brassicae (Phytomyxea, Rhizaria) is one of the economically most important diseases of Brassica crops. The formation of hypertrophied roots accompanied by altered metabolism and hormone homeostasis is typical for infected plants. Not all roots of infected plants show the same phenotypic changes. While some roots remain uninfected, others develop galls of diverse size. The aim of this study was to analyse and compare the intra-plant heterogeneity of P. brassicae root galls and symptomless roots of the same host plants (Brassica oleracea var. gongylodes) collected from a commercial field in Austria using transcriptome analyses.\n\nResultsTranscriptomes were markedly different between symptomless roots and gall tissue. Symptomless roots showed transcriptomic traits previously described for resistant plants. Genes involved in host cell wall synthesis and reinforcement were up-regulated in symptomless roots indicating elevated tolerance against P. brassicae. By contrast, genes involved in cell wall degradation and modification processes like expansion were up-regulated in root galls. Hormone metabolism differed between symptomless roots and galls. Brassinosteroid-synthesis was down-regulated in root galls, whereas jasmonic acid synthesis was down-regulated in symptomless roots. Cytokinin metabolism and signalling were up-regulated in symptomless roots with the exception of one CKX6 homolog, which was strongly down-regulated. Salicylic acid (SA) mediated defence response was up-regulated in symptomless roots, compared with root gall tissue. This is probably caused by a secreted benzoic acid salicylic acid methyl transferase from the pathogen (PbBSMT), which was one of the highest expressed pathogen genes in gall tissue. The PbBSMT derived Methyl-SA potentially leads to increased pathogen tolerance in uninfected roots.\n\nConclusionsInfected and uninfected roots of clubroot infected plants showed transcriptomic differences similar to those previously described between clubroot resistant and susceptible hosts. The here described intra-plant heterogeneity suggests, that for a better understanding of clubroot disease targeted, spatial analyses of clubroot infected plants will be vital in understanding this economically important disease.

plant biology↗

bioRxiv2018

Biotrophic interactions disentangled: In-situ localisation of mRNAs to decipher plant and algal pathogen - host interactions at single cell level.

Plant-pathogen interactions follow spatiotemporal developmental dynamics where gene expression in pathogen and host undergo crucial changes. It is of great interest to detect, quantify and localise where and when key genes are active or inactive. Here, we adapt single molecule FISH techniques to demonstrate presence and activity of mRNAs using phytomyxids in their plant and algal host from laboratory and field materials. This allowed to monitor and quantify the expression of genes from the clubroot pathogen Plasmodiophora brassicae, several species of its Brassica hosts, and of several brown algae, including the genome model Ectocarpus siliculosus, infected with the phytomyxid Maullinia ectocarpii. We show that mRNAs are localised along a spatiotemporal gradient, thus providing proof-of-concept of the usefulness of these methods. These methods are easily adaptable to any interaction between microbes and their algal or plant host, and have the potential to increase our understanding of processes underpinning complex plant-microbe interactions.

plant biology↗

bioRxiv2018

PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery

Patient-derived tumor xenograft (PDX) mouse models are a versatile oncology research platform for studying tumor biology and for testing chemotherapeutic approaches tailored to genomic characteristics of individual patients tumors. PDX models are generated and distributed by a diverse group of academic labs, research organizations, multi-institution consortia, and contract research organizations. The distributed nature of PDX repositories and the use of different standards in the associated metadata presents a significant challenge to finding PDX models relevant to specific cancer research questions. The Jackson Laboratory and EMBL-EBI are addressing these challenges by co-developing PDX Finder, a comprehensive open global catalog of PDX models and their associated datasets. Within PDX Finder, model attributes are harmonized and integrated using a previously developed community minimal information standard to support consistent searching across the originating resources. Links to repositories are provided from the PDX Finder search results to facilitate model acquisition and/or collaboration. The PDX Finder resource currently contains information for more than 1900 PDX models of diverse cancers including those from large resources such as the Patient-Derived Models Repository, PDXNet, and EurOPDX. Individuals or organizations that generate and distribute PDXs are invited to increase the \"findability\" of their models by participating in the PDX Finder initiative at www.pdxfinder.org.

cancer biology↗