Pilar Junier

Université de Neuchâtel | UniNE ·  Laboratoire de microbiologie

Microbiology is a difficult topic to teach given that the objects of study are mostly invisible to the learner. The majority of university students beginning their training in biology are more interested in natural objects that can be seen with the naked eye. Nonetheless, microorganisms are key components of the biosphere and a good microbiological...

Extreme environments on Earth host a large diversity of microbial life. Bacteria, archaea, and fungi are able to survive under one or several extreme conditions including extreme ranges of temperature, pressure, pH or salinity. Despite extensive research on extremophilic microorganisms, a relatively unexplored frontier within the study of the deep...

This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The “fungal drops” method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µL drops on a hydrophobic su...

In the last ten years, blooms of benthic cyanobacteria producing derivatives of the potent neurotoxin anatoxin-a have been repeatedly reported in rivers of temperate regions all over the world. For three series of events, in New Zealand, the USA, and Canada, a cohesive cluster of Microcoleus strains was found to be responsible for the toxin synthes...

Dissolved organic matter and microorganisms were analyzed along the flow path of a geothermal facility in Austria. Various analytical methods were used to characterize and differentiate between natural and synthetic organic matter, characterize the microbial community composition, and determine the implications of microorganisms in an operating a g...

Microbiology is a difficult topic to teach given that the objects of study are for the most invisible to the learner. The majority of university students starting their training in biology are more interested in natural objects that can be seen with the naked eye. Nonetheless, microorganisms are key components of the biosphere and a good microbiolo...

True morels ( Morchella spp.) are a diverse fungal genus with more than 80 recognized species that show high continental endemism. The cultivation of Asian morel isolates in Europe is becoming more common in Switzerland and other European countries, however, the impact this may have on the diversity of native morel populations remains unknown. In o...

As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), myc...

Fungi of the genus Aspergillus are widespread in the environment where they produce large quantities of airborne conidia. Inhalation of Aspergillus spp. conidia in immunocompromised individuals can cause a wide spectrum of diseases, ranging from hypersensitivity responses to lethal invasive infections. Upon deposition in the lung epithelial surface...

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 st...

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other env...

The production of specialized resting cells is a remarkable survival strategy developed by many organisms to withstand unfavourable environmental factors such as nutrient depletion or other changes in abiotic and/or biotic conditions. Five bacterial taxa are recognized to form specialized resting cells: Firmicutes, forming endospores ; Actinobacter...

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 heterogen...

Resistant cells, such as spores are a vital part of the life cycle of fungi with essential roles in ecology and reproduction. These structures help fungi not only to disperse to other environments but also to survive long periods of time awaiting favorable growth conditions. As a result, fungal spores and resistant cells are part of the microbial s...

Background 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” may be driven both by mycelial physical properties and by interactions between bacteria and f...

Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognised as key components of the microbiome in other eukaryotes, such as humans, whe...

Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexual reproduction in fungi is controlled by mating-type ( MAT...

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 theoret...

Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.

Endosporulation is a complex morphophysiological process resulting in a more resistant cellular structure that is produced within the mother cell and is called endospore. Endosporulation evolved in the common ancestor of Firmicutes, but is lost in descendant lineages classified as asporogenic. While Kurthia spp. is considered to comprise only aspor...

Dissolved organic matter (DOM) can be found in a variety of deep subsurface environments such as sedimentary basins, oil fields and mines. However, the origin, composition and fate of DOM within deep geothermal reservoirs used for energy production is relatively unknown. With well depths reaching a few kilometers, these sites give access to investi...

This data was collected to write an extensive review on organic compounds in geothermal fluids as part of the REFLECT (Redefining geothermal fluid properties at extreme conditions to optimize future geothermal energy extraction). The data is mainly focussed on geothermal sites were organic compound data was reported in the literature. It includes d...

Several bacteria have long been known to interact intimately with fungi, but molecular approaches have only recently uncovered how cosmopolitan these interactions are in nature. Currently, bacterial–fungal interactions (BFI) are inferred based on patterns of co-occurrence in amplicon sequencing investigations. However, determining the nature of the...

In most habitats, fluctuating environmental conditions create periods of compromised survival for metabolically active organisms. In response, various survival strategies have evolved, including the formation of resilient resting cells. We assessed the biodiversity of the lysis‐resistant bacteria in three different environments by applying a harsh...

To disseminate 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 und...

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores...

Bacterial-fungal interactions (BFI) play a major role on ecosystem functioning and might be particularly relevant at a specific development stage. For instance, in the case of biological control of fungal pathogens by bacteria, a highly relevant kind of BFI, in-vitro experiments often assess the impact of a bacterium on the inhibition of actively g...

Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, whic...

In recent years, microfluidic technologies have become widespread in biological science. However, the suitability of this technique for understanding different aspects of spore research has hardly been considered. Herein, we review recent developments in 'spores-on-a-chip' technologies, highlighting how they could be exploited to drive new frontier...

Background Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PC...

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 heterogen...

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s 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 drive...

Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogen...

Microbiology is an essential element of our everyday lives. This is not only the consequence of the importance of some pathogenic microorganisms, but also due to their positive and important role in processes related to human health, food production or waste recycling, to cite a few. However, the relevance of microbiology for the well-being of huma...

The oxalate-carbonate pathway (OCP) is a biogeochemical process linking oxalate oxidation and carbonate precipitation. Currently, this pathway is described as a tripartite association involving oxalogenic plants, oxalogenic fungi, and oxalotrophic bacteria. While the OCP has recently received increasing interest given its potential for capturing ca...

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s 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 drive...

Routinely, fungal–fungal interactions (FFI) are studied on agar surfaces. However, this format restricts high-resolution dynamic imaging. To gain experimental access to FFI at the hyphal level in real-time, we developed a microfluidic platform, a FFI device. This device utilises microchannel geometry to enhance the visibility of hyphal growth and p...

Bacteria-fungi interactions (BFI) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions, but also by the physicochemical constraints and three dimensional structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activit...

The composition of the cheese microbiome has an important impact on the sensorial quality and safety of cheese. Therefore, much effort has been made to investigate the microbial community composition of cheese. Quantitative real-time polymerase chain reaction (qPCR) is a well-established method for detecting and quantifying bacteria. High-throughpu...

Fungal diseases are currently affecting a record number of people around the globe, with the genus Aspergillus representing one of the most prevalent groups of opportunistic fungal pathogens. Many aspects of the ecology of Aspergillus spp. are linked to pathogenicity, but so far, the ability to enhance their infectious potential by manipulating the...

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...

We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microb...

This study evaluates mechanisms of biogenic mineral formation induced by bacterial iron reduction for the stabilization of corroded iron. As an example, the Desulfitobacterium hafniense strain TCE1 was employed to treat corroded coupons presenting urban natural atmospheric corrosion, and spectroscopic investigations were performed on the samples’ c...

Among the phylum Firmicutes, members of the genus Bacillus are probably the most extensively studied as beneficial microorganisms with application in agroecology. However, members of other genera within the Phylum are equally important. This chapter highlights the beneficial role of members of the phylum Firmicutes, with the exception of Bacillus s...

Background Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing errors...

The effect of three plant growth-promoting Bacillus strains inoculated either alone or as a consortium was tested on oat (Avena sativa) growth. The bioinoculants were applied as vegetative cells or endospores at low cell densities on the seeds and their effect was tested in sterile in vitro conditions, pot experiments, and a field trial. The in vit...

While often considered as harmful for cultural heritage, microorganisms can also be used for its safeguarding. The methods used so far for the conservation-restoration of cultural heritage are often unsatisfactory in terms of efficiency and durability. Inhibitors or complexing agents are also toxic and pose potential threats to human health and to...

Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament’s supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the...

Archaeological iron artefacts encounter serious post-excavation problems when contaminated with salts. In fact, once excavated, the exposure to a higher oxygen concentration and lower relative humidity renders the corrosion crust formed during burial no longer stable. In particular, the process is induced by chloride ions and flakes, cracks and fin...

Background. Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing error...

Background. Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing error...

Here my poster for the Electromicrobiology 2019 symposium in Aarhus Denmark

Volcanos are extreme environments with elevated temperatures, ranging from 45°C to 120°C, low pH(between 1.5 and 2.5), high pressure and high concentration of heavy metals. Fumaroles, the vents fromwhich escape hot gases, present high temperatures around 100°C and a very acidic pH around 2.Although these environments are extreme, evidence from lite...

In this study we investigated how the source of organic carbon (Corg) and nitrogen (Norg) affects the interactions between fungi of the genus Morchella and bacteria dispersing along their hyphae (fungal highways; FH). We demonstrated that bacteria using FH increase the hydrolysis of an organic nitrogen source that only the fungus can degrade. Using...

Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime ex...

Microbiology can greatly help in the quest for a sustainable solution to the problem of iron corrosion, which causes important economic losses in a wide range of fields, including the protection of cultural heritage and building materials. Using bacteria to transform reactive and unstable corrosion products into more-stable compounds represents a p...

There is a pressing need to develop sustainable and efficient methods to protect and stabilize iron objects. To develop a conservation-restoration method for corroded iron objects, this bio-protocol presents the steps to investigate reductive dissolution of ferric iron and biogenic production of stabilizing ferrous iron minerals in the strict anaer...

Marine and lacustrine archaeological waterlogged wood encounters serious problems after excavation due to the accumulation of sulfur and iron compounds during burial. Exposure of these compounds to oxygen results in precipitation of salts and acidification, which can lead to serious structural damage, and ultimately the loss of important cultural h...

Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of th...