Publications by authors named "Roland Marmeisse"

By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome.

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Article Synopsis
  • - Herbaria, which are collections of plant specimens mainly from the 19th and 20th centuries, are valuable for studying the history and evolution of plant pathogens.
  • - Recent advancements in high-throughput sequencing technologies have transformed how researchers analyze ancient pathogens, particularly viruses, enabling the reconstruction of historical viral genomes and enhancing our understanding of plant virus ecology.
  • - The chapter lays out a specific method for isolating and reconstructing ancient viral sequences from degraded DNA found in herbarium plants and their surrounding soil, utilizing Illumina sequencing and de novo assembly to identify relevant viral DNA.
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Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network.

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Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.

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The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either or trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform.

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Article Synopsis
  • Pollution from toxic metals harms soil and water quality, affecting the health of all organisms, including microbes.
  • A metagenomics approach was used to identify genes for metal tolerance from contaminated sites, focusing on cadmium (Cd) resistance in yeast.
  • The gene PLCc43 was found to provide significant Cd tolerance and showed potential for detoxifying other metals, suggesting it could be a useful biomarker for environmental contamination.
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Sugar transporters are essential components of carbon metabolism and have been extensively studied to control sugar uptake by yeasts and filamentous fungi used in fermentation processes. Based on published information on characterized fungal sugar porters, we show that this protein family encompasses phylogenetically distinct clades. While several clades encompass transporters that seemingly specialized on specific "sugar-related" molecules (e.

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In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community.

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The microbiota inhabiting in metal polluted environment develops strong defense mechanisms to combat pollution and sustain life. Investigating the functional genes of the eukaryotic microbiota inhabiting in these environments by using metatranscriptomics approach was the focus of this study. Size fractionated eukaryotic cDNA libraries (library A, < 0.

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Constant addition of heavy metal pollutants in soil resulting from anthropogenic activities can prove detrimental to both macro and micro life forms inhabiting the ecosystem. The potential functional roles of eukaryotic microbes in such environment were explored in this study by metatranscriptomics approach. Sized eukaryotic cDNA libraries, library A (<0.

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Environmental pollution through heavy metals is an upcoming universal problem that relentlessly endangers human health, biodiversity and ecosystems. Hence remediating these heavy metal pollutants from the environment by engineering soil microbiome through metatranscriptomics is befitting reply. In the present investigation, we have constructed size fractionated cDNA libraries from eukaryotic mRNA of cadmium (Cd) contaminated soil and screened for Cd tolerant genes by yeast complementation system by using Cd sensitive ycf1 mutant.

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Release of heavy metals into the soil pose a significant threat to the environment and public health because of their toxicity accumulation in the food chain and persistence in nature. The potential of soil microbial diversity of cadmium (Cd) contaminated site was exploited through functional metatranscriptomics by construction of cDNA libraries A (0.1-0.

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Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds.

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Article Synopsis
  • Scientists are studying tiny living things called eukaryotic microorganisms from different environments to learn about their genes, many of which we don't know yet.
  • They can extract a special type of genetic material (mRNA) from these organisms found in nature and use it to create libraries of genes.
  • By using new technologies, researchers hope to discover a lot about how these microorganisms work and what they can do.
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To clarify the early molecular interaction between ectomycorrhizal partners, we performed a RNA-Seq study of transcriptome reprogramming of the basidiomycete Hebeloma cylindrosporum before symbiotic structure differentiation with Pinus pinaster. Mycorrhiza transcriptome was studied for comparison. By reference to asymbiotic mycelium, 47 and 46 genes were specifically upregulated over fivefold (p ≤ 0.

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Metallothioneins are cysteine-rich proteins, which function as (i) metal carriers in basal cell metabolism and (ii) protective metal chelators in conditions of metal excess. Metallothioneins have been characterized from different eukaryotic model and cultivable species. Presently, they are categorized in 15 families but evolutionary relationships between these metallothionein families remain unresolved.

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Functions expressed by eukaryotic organisms in soil can be specifically studied by analyzing the pool of eukaryotic-specific polyadenylated mRNA directly extracted from environmental samples. In this chapter, we describe two alternative protocols for the extraction of high-quality RNA from soil samples. Total soil RNA or mRNA can be converted to cDNA for direct high-throughput sequencing.

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Metallothioneins (MTs) are small, cysteine-rich peptides involved in intracellular sequestration of heavy metals in eukaryotes. We examined the role in metal homeostasis and detoxification of an MT from the ectomycorrhizal fungus Pisolithus albus (PaMT1). PaMT1 encodes a 35 amino acid-long polypeptide, with 7 cysteine residues; most of them part of a C-x-C motif found in other known basidiomycete MTs.

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Extracellular proteins play crucial roles in the interaction between mycorrhizal fungi and their environment. Computational prediction and experimental detection allowed identification of 869 proteins constituting the exoproteome of Hebeloma cylindrosporum. Small secreted proteins (SSPs) and carbohydrate-active enzymes (CAZymes) were the two major classes of extracellular proteins.

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To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose.

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Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes.

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Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities.

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Arbuscular mycorrhizal fungi (AMF), which form an ancient and widespread mutualistic symbiosis with plants, are a crucial but still enigmatic component of the plant micro biome. Nutrient exchange has probably been at the heart of the success of this plant-fungus interaction since the earliest days of plants on land. To characterize genes from the fungal partner involved in nutrient exchange, and presumably important for the functioning of the AM symbiosis, genome-wide transcriptomic data obtained from the AMF Rhizophagus irregularis were exploited.

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Background: Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by standard methods are represented by truncated cDNAs due to premature stoppage of reverse transcriptase activity and preferential cloning of short cDNAs.

Results: We report here a simple and cost effective technique for preparation of sized eukaryotic cDNA libraries from as low as three microgram of total soil RNA dominated by ribosomal and bacterial RNA.

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Article Synopsis
  • Scientists used a special technique to find out which genes are important for a fungus called Hebeloma cylindrosporum to form mycorrhizas, which are like helpful connections between the fungus and plant roots.
  • They discovered a mutant version of the fungus that couldn’t form mycorrhizas well, especially when certain sugars were present, showing that something was wrong with its ability to grow properly with plants.
  • After studying the genes, they found one important gene called HcMycE1 that helps the fungus create mycorrhizal structures, and when this gene was interrupted, the fungus couldn’t form those helpful connections with the plants.
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