Biology subjects

Schostag, M. D.

Publications and source records attributed to Schostag, M. D..

8 recordsLinked to original sources

bioRxiv2026

Multi-omics reveals mechanisms behind pathogen inhibition by a microalgal microbiome

Aquaculture is an essential food production sector for meeting the global demand for high-quality protein. However, the sector faces significant challenges from bacterial pathogens, particularly Vibrio anguillarum, which causes vibriosis in numerous commercially important fish species. Current disease management strategies rely heavily on antibiotics, leading to antimicrobial resistance and environmental concerns. Microalgal microbiomes represent promising alternatives for sustainable pathogen control, yet the molecular mechanisms underlying their inhibitory activity remain poorly understood. Here, we employed an integrated multi-omics approach to elucidate the mechanisms by which the microbiome of microalga Isochrysis galbana inhibits the highly virulent fish pathogen V. anguillarum strain 90-11-286. Using a GFP-based inhibition assay, we confirmed potent pathogen suppression by the algal microbiome, achieving complete inhibition at a 1:1000 ratio of pathogen to microbiome. Through 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and metabolomics, we characterized community composition, genomic potential, gene expression patterns, and metabolite production during pathogen challenge. The inhibitory microbiome was dominated by Alteromonas macleodii and Vreelandella alkaliphila, with high-quality metagenome-assembled genomes revealing substantial secondary metabolite biosynthetic potential. Metatranscriptomic analysis revealed active expression of biosynthetic gene clusters encoding, for example, non-ribosomal peptide synthetases, particularly a siderophore gene cluster in V. alkaliphila. Metabolomic profiling confirmed the production of hydroxamate siderophores in the microbiome, including desferrioxamine analogues, proferrioxamine G1t, and tenacibactin D, which accumulated during pathogen inhibition, as well as 10 putative new compounds. Notably, siderophore production was constitutive rather than pathogen-induced, suggesting iron competition as the primary inhibitory mechanism. Our findings demonstrate that iron sequestration through siderophore production represents a key strategy for pathogen suppression in marine microbial communities. This work provides molecular evidence for microbiome-mediated disease control and establishes a foundation for developing rationally designed multi-strain probiotic consortia for sustainable aquaculture applications, offering an environmentally friendly alternative to antibiotic-based pathogen management strategies.

microbiology↗

bioRxiv2025

Penicillium hordei acidification precipitates Bacillus subtilis lipopeptides to evade inhibition

Interkingdom interactions are crucial for community and ecosystem functioning, however secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Penicillium and Bacillus species can individually suppress soilborne phytopathogens and promote plant growth. Here, we showed that Penicillium hordei and Bacillus subtilis co-culture led to precipitation of B. subtilis lipopeptides, observed as white line in agar. Metabolomic analysis revealed B. subtilis triggered enhanced production of fungal terrestric acid and its biosynthetic intermediates, which induced lipopeptide precipitation to prevent P. hordei inhibition by chemical inactivation and physical barrier formation. Besides lipopeptide precipitation, terrestric acid-mediated acidification progressively reduced production of antifungal plipastatins. The lack of lipopeptide production permitted P. hordei to invade and overgrow B. subtilis colony. We demonstrated that the white line phenomenon was conserved among closely related fungi via secretion of terrestric, fulvic or barceloneic acids. Furthermore, terrestric acid at specific concentrations acted as a universal metabolite that drives B. subtilis lipopeptide precipitation even in distantly related fungi. This study provides new insights into acidification as a fungal defensive strategy that may promote co-existence with beneficial bacteria exhibiting strong antagonistic potential, thereby contributing to the formation of a stable rhizosphere community.

microbiology↗

bioRxiv2025

Genetic memory devices to detect specialized metabolites in plant and soil microbiomes

Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, non-disruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 {Delta}all-{Phi} strain. Additionally, the four sensors were shown to respond to their cognate ligand in a non-sterile soil extract medium containing the diverse microbiome found in soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of real-time biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.

microbiology↗

bioRxiv2024

Secondary metabolites shape Streptomyces-Streptomyces interaction: Mass Spectrometry Imaging reveals lydicamycins broadly induce sporulation

Streptomyces are major players in soil microbiomes, however, interactions involving Streptomyces and other actinobacteria are rarely described. The complex developmental cycle of actinobacteria necessitates a multi-omics approach to unravel the web of information. This study resulted from the observation of induced morphogenesis between two environmental isolates from the same site, Kitasatospora sp. P9-2B1 and Streptomyces sp. P9-2B2. When co-cultivated on potato dextrose agar (PDA), P9-2B2 induced a wave-like sporulation in strain P9-2B1. Using mass spectrometry imaging, we revealed that a suite of lydicamycins were present in this induced sporulation zone. Lydicamycin deficient mutants were generated using CRISPR Base-Editing and the inducible sporulation ceased, confirming their role in triggering morphological differentiation. In agar diffusion assays, pure lydicamycin was inhibitory when added concurrently with bacterial inoculation and induced sporulation with delayed addition. Subsequent testing of additional environmental isolates resulted in the same inducible sporulation wave phenomenon, including Streptomyces coelicolor M145 and M1146. Using transcriptomics, we observed the differential expression of genes related to early aerial mycelium development four days into cocultivation and the transitional genes responsible for development of spores on day 9. Along with these differentially expressed genes, we also observed numerous overall stress responses, specifically cell envelope stress responses. These findings uncovered actinobacteria interactions mediated by lydicamycins, pointing to a potential role of certain groups of bioactive metabolites in nature. ImportanceShifting away from an antibiotic discovery mindset, uncovering the chemical ecology of secondary metabolites is key to maximizing their biotechnological application. The reduced complexity of dual cultures allows for in depth analysis and investigation of these interactions via multi-omics provides orthogonal data leading to more robust conclusions. This study provides insight into the role of lydicamycins in dual cultures with other actinobacteria and provides an integral roadmap for future chemical ecology work between microorganisms, especially through the use of mass spectrometry imaging.

ecology↗

bioRxiv2023

Concurrent stimulation of diflufenican biodegradation and changes in the active microbiome in gravel revealed by Total RNA

The use of slowly degrading pesticides poses a particular problem when these are applied to urban areas such as gravel paths. The urban gravel provides an environment very different from agricultural soils; i.e., it is both lower in carbon and microbial activity. We, therefore, endeavoured to stimulate the degradation of the pesticide diflufenican added to an urban gravel microcosm amended with dry alfalfa to increase microbial activity. In the present study, the formation of the primary diflufenican metabolite 2-[3-(Trifluoromethyl)phenoxy]nicotinic acid (commonly abbreviated as AE-B) was stimulated by the alfalfa amendment. The concurrent changes of the active microbial communities within the gravel were explored using shotgun metatranscriptomic sequencing of ribosomal RNA and messenger RNA. Our results showed, that while the active microbial communities in the gravel were dominated by bacteria with a relative abundance of 87.0 - 98.5 %, the eukaryotic groups, fungi and micro-eukaryotes, both had a 4-5 fold increase in relative abundance over time in the alfalfa amended treatment. Specifically, the relative abundance of microorganisms involved in degradation of complex carbon sources, Bacteroidetes, Verrucomicrobia, Sordariomycetes, Mortierellales, and Tremellales, were shown to increase in the alfalfa amended treatment. Further, the functional gene profile showed an increase in genes involved in increased activity and production of new biomass in the alfalfa treatment compared to the control, as well as pointing to genes potentially involved in biodegradation of complex carbon sources and the biotransformation of diflufenican.

microbiology↗

bioRxiv2023

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin in an antagonistic interaction with Pseudomonas marginalis. The presence of bacillibactin strongly influenced the outcome of the interaction in an iron-dependent manner. The bacillibactin producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of bacillibactin restricted B. subtilis colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our analysis revealed that the Bacillus-Pseudomonas interaction is conserved across fluorescent Pseudomonas spp., expanding our understanding of the interplay between two genera of the most well-studied soil microbes.

microbiology↗

bioRxiv2021

Complete genome sequence and Benzophenone-3 mineralisation potential of Rhodococcus sp. USK10, a bacterium isolated from riverbank sediment.

Benzophenone-3 (BP3) is an organic UV filter whose presence in the aquatic environment has been linked to detrimental developmental impacts in aquatic organisms such as coral and fish. The genus Rhodococcus has been extensively studied and is known for possessing large genomes housing genes for biodegradation of a wide range of compounds, including aromatic carbons. Here, we present the genome sequence of Rhodococcus sp. USK10, which was isolated from Chinese riverbank sediment and is capable of utilising BP3 as the sole carbon source, resulting in full BP3 mineralisation. The genome consisted of 9,870,030 bp in 3 replicons, a G+C content of 67.2%, and 9,722 coding DNA sequences (CDSs). Annotation of the genome revealed that 179 of these CDSs are involved in metabolism of aromatic carbons. The complete genome of Rhodococcus sp. USK10 is the first complete, annotated genome sequence of a Benzophenone-3 degrading bacterium. Through radiolabelling, it is also the first bacterium proven to mineralise Benzophenone-3. Due to the widespread environmental prevalence of Benzophenone-3, coupled to its adverse impact on aquatic organisms, this characterisation provides an integral first step in better understanding the environmentally relevant degradation pathway of the commonly used UV filter. Given USK10s ability to completely mineralise Benzophenone-3, it could prove to be a suitable candidate for bioremediation application.

genomics↗

bioRxiv2019

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome

BackgroundArctic surface soils experience pronounced seasonal changes in temperature and chemistry. However, it is unclear how these changes affect microbial degradation of organic matter, nitrogen cycling and microbial stress responses. We combined measurements of microbiome transcriptional activity, CO2 production, and pools of carbon and nitrogen to investigate the microbial response to warming in the laboratory, from -10 {degrees}C to 2 {degrees}C, and subsequent cooling, from 2 {degrees}C to -10 {degrees}C, of a high Arctic tundra soil from Svalbard, Norway.\n\nResultsGene expression was unaffected by warming from -10 {degrees}C to -2 {degrees}C and by cooling from -2 {degrees}C to -10 {degrees}C, while upon freezing (2 {degrees}C to -2 {degrees}C) a defense response against oxidative stress was observed. Following modest transcriptional changes one day after soil thaw, a more pronounced response was observed after 17 days, involving numerous functions dominated by an upregulation of genes involved in transcription, translation and chaperone activity. Transcripts related to carbohydrate metabolism and degradation of complex polymers (e.g. cellulose, hemicellulose and chitin) were also enhanced following 17 days of soil thaw, which was accompanied by a four-fold increase in CO2 production. In addition, anaerobic ammonium oxidation and turnover of organic nitrogen were upregulated. In contrast, nitrification, denitrification and assimilatory nitrate reduction were downregulated leading to an increase in the concentration of soil inorganic nitrogen.\n\nConclusionthe microorganisms showed negligible response to changes in sub-zero temperatures and a delayed response to thaw, which after 17 days led to upregulation of soil organic matter degradation and enhanced CO2 production, as well as downregulation of key pathways in nitrogen cycling and a concomitant accumulation of inorganic nitrogen available for plants.

microbiology↗