Post-doctoral position (M/F) in metagenomics of digestive microbial communities

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Post-doctoral position (M/F) in metagenomics of digestive microbial communities

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Job description

Offer DescriptionThe post-doctoral position is part of an ANR project studying the influence of the digestive microbiota of detritivores on the decomposition of leaf litter in freshwater ecosystems (DIET project ).The process of plant litter decomposition is central to the carbon cycle, and freshwater environments have been shown to significantly contribute to this process on a global scale. Numerous functional ecology studies have focused on the role of detritivores (macro-invertebrates that break up dead leaves) and their metabolic capacities to degrade lignocellulose, because the action of these decomposer organisms is required for the carbon and nutrients contained in the leaves to be transferred to other compartments of the ecosystem. However, these detritivores have been considered at the scale of the ‘holobiont’, so their intrinsic role has never been discriminated from that of their digestive microbiota, which limits our understanding of this ecosystemic process.The aim of this project is therefore to assess the influence of the digestive microbiota of detritivores on the decomposition of plant litter and the resulting carbon flows in freshwater environments. To do this, the postdoc will apply metagenomic and isotopic approaches to the digestive microbial communities of detritivorous isopods (a biological model used for the past fifteen years in the host team), in order to determine whether their digestive tract is a bioreactor for the degradation process.The postdoc will be responsible for the functional characterisation of the digestive microbiota of isopods using a metagenomic approach. The priority will be to identify the lignocellulose degradation genes present in the digestive microbiota metagenome, on several individuals for around ten species. This dataset will also allow to estimate the inter-indiviudal and inter-species variability in the gene repertoires of the detritivore microbiota, and thus to estimate whether there is a core repertoire of degradation genes in these digestive communities.The postdoc will also be responsible for developing an experimental DNA isotope labelling approach (DNA-SIP) to identify which species in the digestive microbiota effectively degrade plant compounds, and whether these key species vary between detritivores. These data will be used to estimate the level of functional redundancy in communities active in the degradation of plant compounds.To carry out these tasks successfully, the postdoc will be able to draw on the laboratory’s Molecular Ecology platform, as well as on a bioinformatics engineer recruited for the same ANR project in order to support the management and analysis of the sequencing data.– Acquisition of metagenomic data (most likely using Nanopore long-read technology) on the digestive communities of isopods collected in situ.– Development and implementation of the DNA-SIP protocol– Experiments under controlled and sterile conditions– Analysis of sequencing data: characterisation of the functional repertoire of digestive communities, focus on lignocellulose-degrading enzymes (CAZymes), gene annotation, comparative analyses (inter-individual, inter-species).– Ensuring the traceability and reproducibility of molecular biology and bioinformatics analyses.– Communicating results and writing publications– Possibility of supervising a Masters trainee as part of the ANR project.The postdoc will be based at LEHNA (Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés) at Lyon 1 University, on the Doua campus. Through the BioEEnViS research federation, our laboratory provides access to molecular biology platforms, experimental areas under sterile conditions and a computing cluster. Several metagenomics projects are currently being developed in the laboratory, providing a stimulating and supportive working environment.This position is available for 22 to 30 months (depending on experience), funded as part of an ANR JCJC project (2023-2027). Salary according to CNRS salary scale (experience taken into account). The position is to be filled from February 2025, and as soon as possible.Where to apply WebsiteRequirementsResearch Field Biological sciences Education Level PhD or equivalentResearch Field Environmental science Education Level PhD or equivalentLanguages FRENCH Level BasicResearch Field Biological sciences Years of Research Experience NoneResearch Field Environmental science Years of Research Experience NoneAdditional InformationEligibility criteriaDifferent profiles may be suitable for this position:
Solid skills in molecular biology applied to next-generation sequencing technologies (DNA extractions, preparation of sequencing libraries). A background in bioinformatics, which you would like to develop with in-house support.
Solid skills in bioinformatics analysis of (meta)genomic data (assembly, gene annotation, design and implementation of scripts and pipelines, use of a computing cluster). A background in molecular biology, which you would like to develop with in-house support.– Curiosity about the interdisciplinary aspect of the project, and the desire to learn new approaches to complement your skills.– Ability to work as part of a team– AutonomyExperience in DNA-SIP, as well as skills in microbiology, are not required but will be considered as assets.Website for additional job detailsWork Location(s)Number of offers available 1 Company/Institute Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Country France City VILLEURBANNE GeofieldContact CityVILLEURBANNE WebsiteSTATUS: EXPIREDShare this page

Expected salary

Location

Villeurbanne, Rhône

Job date

Sat, 28 Dec 2024 00:59:25 GMT

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