Biology subjects

Junier, P.

Publications and source records attributed to Junier, P..

15 recordsLinked to original sources

bioRxiv2026

Methods for evaluating bacterial dispersal on hyphal networks

In heterogeneous environments, the hyphae of filamentous fungi and oomycetes can facilitate the dispersal of other microorganisms. The use of these "fungal highways" (FH) is regulated by both physical and biological factors with their interplay resulting in variable capabilities of different microbes to establish FH. Several devices have been developed to test the movement of bacteria across mycelium. However, these methods are usually time-consuming and cannot be applied either at a large scale or in a high throughput format. In this study, we developed 3D-printed experimental devices that physically separate two environments while allowing hyphal networks to act as bridges for bacterial movement. The final design allows for the simultaneous testing of up to 10 pairs and the inclusion of any culturing media. With these devices, we investigated how fungal-bacterial pairing, nutrient conditions, and inoculation strategies influence FH formation. Bacterial transport was limited in nutrient-rich media but increased under poorer nutrient conditions, consistent with enhanced exploratory growth of the mycelium. Both cis- and trans-inoculation supported FH formation, although bacterial arrival was delayed in the absence of co-inoculation. The devices were used to demonstrate that transport of bacteria by FH was relevant for the colonization of a natural substrate. Finally, we established a novel in planta assay to evaluate FH formation during host colonization. This assay demonstrated that Fusarium graminearum can transport bacteria during wheat spike colonization. Together, these results provide accessible, scalable tools to study hyphal-mediated bacterial dispersal and highlight the combined role of biological specificity and nutrient context in the establishment of FH. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/719220v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1cf39aforg.highwire.dtl.DTLVardef@1d41e6corg.highwire.dtl.DTLVardef@1196637org.highwire.dtl.DTLVardef@85cc6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.

Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 {micro}g/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation. Environmental ImplicationPharmaceuticals and their metabolites are environmentally hazardous because these bioactive micropollutants are persistent and continuously discharged via wastewater, thereby endangering both ecosystem and human health. This study shows that pollutant-adapted microbial consortia can address this challenge, retaining strong degradative function across large concentration fluctuations, including environmentally relevant levels. It also demonstrates scalability: the adapted community can be transferred to real-wastewater operation to remove both targeted and additional pharmaceuticals, supporting a bio-based "polishing" step for wastewater treatment plants. Overall, these findings support more sustainable biological mitigation strategies to reduce micropollutant loads.

microbiology↗

bioRxiv2025

A microfluidic platform for the observation and quantification of fungal highways

Soil is a complex system characterised by intra- and inter-kingdom interactions among microbial communities. While many different types of fungal-bacterial interactions have been described, hyphal-mediated transport of bacteria via the so-called "fungal highway" (FH) has not been mechanistically described. Bacteria require a liquid film for active movement; therefore, liquid saturation is a significant limiting factor for their dispersal in soil. Hyphal networks contribute to the connectivity between discrete soil microbial populations by providing a physical network through the unsaturated soil matrix. This network serves as a scaffold for liquid transport, thus allowing bacteria to migrate further or access previously isolated spaces. Studying these interactions is challenging due to the complex and stochastic nature of the soil environment; this "black box" aspect makes it difficult to visualise interactions at the microbial scale. Microfluidic technology can provide a solution by offering precise imaging at a high resolution in a physically and chemically controlled environment. We designed a microfluidic device, the Fungal Highways Device (FHD), that allows us to culture filamentous organisms in unsaturated environments and visualise and quantify bacterial dispersal along hyphal networks at the single-cell level. We showed that Pythium ultimum is essential for Pseudomonas putida movement across an unsaturated environment, and we identified mycelial biomass and hyphal front length as key factors influencing the bacterias movement towards the outlet. We propose that the liquid transport facilitated by P. ultimum mycelium influences the FH behaviour during its interaction with P. putida.

bioengineering↗

bioRxiv2025

Fighting Aspergillus infection using biocontrol bacteria: A proof-of-concept of environmental interference in a translational setting

Aspergillus fungi are opportunistic pathogens that affect millions of people worldwide. Aspergilli produce organic acids to optimize the environmental pH and match the needs of their enzymatic machinery. In this study, we tested the hypothesis that this also occurs during infection. By producing oxalic acid (OA), Aspergillus would manipulate pH during lung infection and thus, interfering with this process could control the pathogen. To test this hypothesis, we assessed in silico the potential for OA production in a wide range of Aspergilli. A genetic marker for AO production was detected in most of the species including prevalent human pathogens. We tested OA production in vitro in four strains of A. niger and A. fumigatus, but only one of the A. niger strains produced OA consistently. For this fungal strain, oxalotrophic bacteria were able to control fungal growth via OA consumption. To translate this observation into a pre-clinical system, increasingly complex experiments were performed. In 3D-cell cultures, A. niger also secreted OA and modified pH and free Ca2+. Co-inoculation of the oxalotrophic bacterium inhibited the development of the fungus. However, biocontrol could not be replicated in Galleria mellonella, which is often used as an infection model. In contrast, the bacterium improved disease score and the absence of oxalate crystals in the lungs in the mouse model. This biocontrol interaction between oxalotrophic bacteria and A. niger represents a paradigm shift in the fight against opportunistic fungal pathogens, where the goal is to render the host environment less permissive to pathogen development One Sentence SummaryDemonstration of biocontrol as a therapeutic concept to combat Aspergillus niger with oxalotrophic bacteria in an animal infection model

microbiology↗

bioRxiv2025

Prevalence of Oxalotrophy in the Human Microbiome

Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly of the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy - the capacity to use oxalate as a source of energy - is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.

microbiology↗

bioRxiv2024

Visualizing Liquid Distribution Across Hyphal Networks with Cellular Resolution

Filamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the Fungal-Fungal Interaction (FFI) microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular hyphal liquid movement can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways.

microbiology↗

bioRxiv2024

Co-isolation of Penicillium citrinum and its cell-switching partner Meyerozyma guilliermondii from a geothermal power plant

Progresses in geothermal energy and deep drilling technologies have opened a new window into the terrestrial subsurface. This provides direct access to deep geothermal fluids used to produce heat and electricity, creating an opportunity to isolate and characterize novel microbial strains from these extreme habitats. In this study, we report the co-isolation of two fungal strains. Penicillium citrinum (strain HEK1) was isolated first and thought to be axenic. However, upon exposure to stress (frost and ethanol), a second strain, corresponding to the dimorphic yeast Meyerozyma guilliermondii (strain HEK2), appeared in HEK1 cultures. Strain HEK2 appeared first in the cultures and was followed by the subsequent re-growth of strain HEK1, underscoring their close relationship. Moreover, strain HEK2, able to switch from yeast cells to pseudohyphae when growing alone, did not produce pseudohyphae when in direct contact with strain HEK1. Altogether, our results indicate an intricate interaction between these strains that may allow them to thrive in the deep subsurface. These two fungi represent the first fungal strains isolated from deep geothermal fluids. Their presence within the fluids was confirmed through molecular analysis. The isolation of these strains emphasizes the importance of considering fungi when investigating microbial diversity in subsurface geothermal environments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/599737v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@fdf699org.highwire.dtl.DTLVardef@148b751org.highwire.dtl.DTLVardef@fb37e9org.highwire.dtl.DTLVardef@113b911_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFirst fungal strains isolated from a geothermal power plant C_LIO_LIThe two fungal strains were co-isolated from a geothermal fluid used for heat production C_LIO_LISurprising isolation of the cell-switching yeast upon stress exposure of an apparently axenic culture of the filamentous fungus C_LIO_LIFungal strains with high resistance to stressors and no apparent competition for carbon sources C_LI

microbiology↗

bioRxiv2024

Microfluidic platform for microbial spore germination studies in multiple growth conditions

Spores are highly resistant dormant cells, adapted for survival and dispersal, that can withstand unfavourable environmental conditions for extended periods of time and later reactivate. Understanding the germination process of microbial spores is important in numerous areas including agriculture, food safety and health, and other sectors of biotechnology. Microfluidics combined with high-resolution microscopy allows to study spore germination at the single-cell level, revealing behaviours that would be hidden in standard population-level studies. Here, we present a microfluidic platform for germination studies where spores are confined to monolayers inside microchambers, allowing the testing of four growth conditions in parallel. This platform can be used with multiple species, including non-model organisms, and is compatible with existing image analysis software. In this study, we focused on three soil dwellers, two prokaryotes and one fungus, and revealed new insights into their germination. We studied endospores of the model bacterium Bacillus subtilis and demonstrated a correlation between spore density and germination in rich media. We then investigated the germination of the obligate-oxalotrophic environmental bacterium Ammoniphilus oxalaticus in a concentration gradient of potassium oxalate, showing that lower concentrations result in more spores germinating compared to higher concentrations. We also used this microfluidic platform to study the soil beneficial filamentous fungus Trichoderma rossicum, showing for the first time that the size of the spores and hyphae increase in response to increased nutrient availability, while germination times remain the same. Our platform allows to better understand microbial behaviour at the single-cell level, under a variety of controlled conditions. One-Sentence SummaryA microfluidic platform developed for spore germination studies in multiple growth conditions provides new insights into the germination of spores at the cellular level from three soil dwellers.

bioengineering↗

bioRxiv2023

A ubiquitous Microcoleus species causes benthic cyanotoxic blooms worldwide

Recently, proliferations of benthic cyanobacteria producing derivatives of anatoxin-a have been reported in rivers all over the world. In three river systems, in New Zealand, the USA, and Canada, a cohesive cluster of Microcoleus strains was responsible for toxin production. Here, we document a similar toxigenic event that occurred at the mouth of the river Areuse in lake Neuchatel (Switzerland) and caused the death of several dogs. Using 16S RNA-based community analysis, we show that riverine benthic communities are dominated by Oscillatoriales and especially by Microcoleus strains. We correlate the detection of one sequence variant with the presence of anatoxin-a derivatives and use metagenomics to assemble a complete circular genome of the strain. The strain is distinct from the ones isolated in New Zealand, the USA, and Canada, but belongs to the same species; it shares significant traits with them, in particular a relatively small genome and incomplete vitamin biosynthetic pathways. Overall, our results suggest that the major anatoxin-a-associated benthic proliferations worldwide can be traced back to a single ubiquitous species, Microcoleus anatoxicus, rather than to a diversity of cyanobacterial lineages. We recommend that this species be monitored internationally in order to help predict and mitigate similar cyanotoxic events.

microbiology↗

bioRxiv2022

Ecology shapes the cyclic dominance games between Escherichia coli strains

Evolutionary game theory has provided various models to explain the coexistence of competing strategies, one of which is the rock-paper-scissors (RPS) game. A system of three Escherichia coli strains--a toxin-producer, a resistant, and a sensitive--has become a classic experimental model for studying RPS games. Previous experimental and theoretical studies, however, often ignored the influence of ecological factors such as nutrients and toxin dynamics on the evolutionary game dynamics. In this work, we combine experiments and modeling to study how these factors affect competition dynamics. Using 3D-printed mini-bioreactors, we tracked the frequency of the three strains in different culturing media and under different flow regimes. Although our experimental system fulfilled the requirements of cyclic dominance, we did not observe clear cycles or long-term coexistence between strains. We found that both nutrients and flow rates strongly impacted population dynamics. In our simulations, we explicitly modeled the release, removal and diffusion of toxin. We showed that the amount of toxin that is retained in the system is a simple indicator that can predict competition outcomes across broad parameter space. Moreover, our simulation results suggest that high rates of toxin diffusion might have prevented cyclic patterns from emerging in our experimental system.

evolutionary biology↗

bioRxiv2022

Design and construction of 3D-printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such "fungal highways" is driven both by mycelial physical properties and by interactions between bacteria and fungi. To understand the role of abiotic elements, we designed and 3D-printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of carrying non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow, but dispersed when co-inoculated with motile cells. By teasing apart the abiotic and biotic dimensions, these 3D-printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.

microbiology↗

bioRxiv2022

Spatial scales of competition and a growth-motility tradeoff interact to determine bacterial coexistence

1.The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility tradeoff. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility tradeoff promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

ecology↗

bioRxiv2021

The role of microbial diversity in the formation of soil organic matter quality and persistence

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earths climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of soil organic matter remain missing. Here we used a model soil system to test the hypothesis that more diverse microbial communities generate more stable soil organic matter. We inoculated microbial communities of varying diversities into an model soil matrix amended with simple carbon, and measured the thermal stability of the resultant soil organic matter. Using a novel data analysis approach with Rock-Eval(R) ramped thermal analysis, we found that microbial community diversity drives the chemical fingerprint of soil organic matter. Bacteria-only and low diversity communities lead to less chemically-diverse and more thermally-labile soil carbon pools than highly diverse communities. Our results provide direct evidence for a link between microbial diversity, molecular complexity and SOM stability. This evidence demonstrates the benefits of managing soils for maximum biological diversity as a means of building persistent SOM stocks. ClassificationBiological Sciences: Ecology

ecology↗

bioRxiv2020

Exploiting oxalotrophic bacteria to control Aspergillus niger lung infections

Aspergillus fungi are opportunistic pathogens that affect a large number of people worldwide. Many aspects of Aspergillus spp. pathogenesis toward humans are known, but their ability to enhance their infectious potential by manipulating the environmental pH of its host has not been considered yet. In this study, we tested the hypothesis that by producing oxalic acid, Aspergillus niger can manipulate pH during lung infection and thus, interfering with this process could limit pathogenicity. To test this hypothesis, we co-cultured A. niger with oxalotrophic bacteria in increasingly complex testing systems (Petri dishes and 3D-cell cultures systems). In in vitro tests, oxalotrophic bacteria limit oxalic acid production and suppressed the pH shift induced by A. niger. In 3D-cell cultures (Transwells(R) and Bronchioles-on-a-chip), A. niger also modified pH, Ca2+ and oxalic acid concentrations. Co-inoculation with as little as 10 cells of the oxalatrophic bacterium strongly inhibited the germination and development of A. niger and returned each of the three parameters to the baseline physiological values of uninfected cells. This biocontrol interaction between oxalotrophic bacteria and oxalate-producing A. niger could represent a paradigm shift in the fight against opportunistic fungal pathogens, where the host environment is rendered less permissive to fungal development.

microbiology↗

bioRxiv2020

Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes

Sporulation is a complex morphophysiological process resulting in a cellular structure that is more resistant than the vegetative form. In Firmicutes, this structure is produced within the mother cell, and is called an endospore. Endospore formation is thought to have evolved in the common ancestor of Firmicutes. However, sporulation has apparently been lost in some extant lineages that are defined as asporogenic. We isolated strain 11kri321, a representative of the genus Kurthia, from an oligotrophic geothermal reservoir. While Kurthia spp. is considered to comprise only asporogenic species, strain 11kri321 produced spores. Genomic reconstruction of the sporulation pathway shows elements typical of sporulation in Bacilli, including the signaling for sporulation onset. However, key genes were missing, including those involved in engulfment and dipicolinic acid synthesis. Based on the results for strain 11kri321, sporulation was investigated in other Kurthia strains. Genes involved in signaling, cell division and spore coat formation were detected in three available Kurthia genomes. Moreover, endosporulation was clearly visualized in at least two of the four strains tested. These results show that Kurthia is an endospore-forming Firmicute lineage. However, the genetic background of sporulation in this genus deviates from the known sporulation pathway in Firmicutes and even within Bacilli, suggesting that a revision of the minimal set of genes used for genomic detection of sporulation is required. Based on our findings we propose the term cryptosporulant to refer to putative asporogenic Firmicutes for which a detailed genomic and physiological characterization of sporulating is missing. ImportanceEndospore-forming Firmicutes include many environmental and medical relevant bacterial clades. In these microorganisms, the ability to produce endospores is essential for survival in the environment and even for pathogenesis. The minimum core of genes required to produce a viable and resistant spore, the distinction between endospore-forming and asporogenic groups, as well as the evolution of sporulation have been a subject of investigation and debate for decades. Here, we demonstrate endosporulation in the genus Kurthia, considered as asporogenic. Morphological, physiological and genomic analyses were undertaken to demonstrate that sporulation is not lost within this lineage. Based on our results we propose a re-examination of the minimal genetic requirements of sporulation and the use of the term cryptosporulant to describe lineages of Firmicutes that have not previously been observed to sporulate, but for which a detailed analysis is still missing.

microbiology↗