Postdoc – metabarcoding & metagenomic based biodiversity monitoring
Project description:
The 2018 Intergovernmental Panel on Climate Change (IPCC) Special Report (SR15) confirmed that we are in a climate crisis, with the past decade recording the ten warmest years since 1850. Rising temperatures and extreme weather events threaten ecosystems, with potential total losses. However, the maintenance of healthy ecosystems is a self-evident prerequisite for conserving biodiversity and for supporting life on earth. Monitoring ecosystems health typically involve indicator taxa and remote sensing, but these provide limited insights into trophic interactions. Plants, as primary producers, underpin ecosystems, and their health is essential for stability. However, plant biomass and quality can be significantly reduced by insect pests and diseases caused by viral or fungal pathogens which are responsible for ~50% and 30% of plant Emerging Infectious Disease (EID) respectively. Climate variations exacerbate these interactions: elevated CO₂ reduces plant nitrogen content, increasing herbivory and pathogen severity, while higher temperatures accelerate insect metabolism and pathogen transmission. Drought stress weakens plant defences, and excessive rainfall promotes fungal infections. The general trend of higher pathogen infections under environmental stress poses a major risk to ecosystems.
Traditional monitoring ecosystem health currently overlooks ecological processes and interactions due to the high cost and time required for comprehensive surveys of plants, fungi, insects, and their pathogens. An alternative and novel approach is to leverage the natural trophic aggregation through trophic-levels: insect herbivores ingest plant viruses and fungi alongside plant material; these insects, along with their fungi and viruses, are then consumed by predatory arthropods (primary consumers), which are subsequently eaten by secondary consumers (usually vertebrates). Additionally, fungi themselves can also be infected by (myco)viruses which can reduce the ability of their fungal hosts to cause disease in plants, an interesting phenomenon known as hypovirulence. This aggregation process was demonstrated in bat guano studies, where most detected viruses originated from insects (up to 61%) and plants or fungi (up to 46%), with mammalian viruses making up less than 10% of the virome.
Over two years, seasonal sampling of bat guano was performed across three climatic zones and two bat species with distinct foraging habits. Insectivorous bats, consuming more than their body weight in prey, serve as ideal aggregator taxa. Two high-throughput sequencing approaches—metagenomics for virome analysis and metabarcoding for plant, arthropod, and fungal identification—were applied to the same samples. The field sampling, lab work and sequencing has been performed. Preliminary analyses of the 2020 dataset enable us to detect no less than 4,660 OTUs for fungi, 1,193 for plants, 5,547 for insects, and 1,590 for viruses. Our objectives are to use trophic, fungal, and viral aggregation in bat guano to assess ecosystem health and understand underlying ecological processes.
Environment:
The person recruited will carry out his/her mission within the ISEM laboratory in Montpellier, under the supervision of a researcher, member of the Institut Universitaire de France (IUF), and in collaboration with a young researcher at CIBIO (Porto, Portugal). The person will spend 2 months a year at CIBIO (funded by the project). Their mission will be carried out as part of the research contract funded by the European Commission and entitled BIOPOLIS (https://www.biopolis.pt/en/).
Main mission:
Researcher will process and analyse high-throughput sequencing data already generated to investigate ecological interactions among viruses, fungi, plants, and insects in bat guano samples, and how they related to abiotic conditions (weather data). They will apply advanced bioinformatics and statistical methods, contribute to scientific publications, and facilitate knowledge transfer through training and outreach at CIBIO.
Activities:
• Pre-process sequencing data: Clean datasets, remove errors, and assign taxonomic status.
• Conduct biodiversity analyses: Calculate species richness, diversity, and evenness indices across taxonomic groups.
• Perform network analyses: Construct association, weighted, and multilayer networks to investigate ecological interactions.
• Statistical models: Use GLMMs and null models to assess environmental and temporal effects on microbial and dietary communities.
• Identify key species: Determine species critical for ecosystem stability and assess potential indicators of ecosystem health.
• Disseminate findings: Publish scientific papers and present at international conferences.
Precise description of the event or the objective result:
• Data Processing & Analysis: Successful completion of the pre-processing, and taxonomic assignment. Deliverable: an annotated script performing these steps and taxonomic abundance table.
• Biodiversity Assessment: Calculation of species richness, diversity, and evenness indices for all taxonomic groups. Deliverable: an annotated script performing these steps and a summary table.
• Network Analyses: Calculations of association, weighted, and multilayer networks to characterise ecological interactions. Deliverable: an annotated script performing these steps and a summary table per model.
• Statistical Modelling: Implementation of GLMMs and null models to evaluate environmental and temporal influences on microbial and dietary communities. Deliverable: an annotated script performing these steps and a summary table per model.
• Identification of Key Species: Determination of species crucial for ecosystem stability and assessment of potential bioindicators. Deliverable: an annotated script performing these steps and a list of species.
• Scientific Dissemination: Writing and submission of at least two peer-reviewed scientific papers and presentation of results at international conferences. Deliverable: two manuscripts submitted.
Net salary:
€2,380 per month
Contract duration:
24 months
Location:
Montpellier (France)
How to apply:
Please send your application or any inquiry to the contact email.
Contact details:
sebastien.puechmaille@umontpellier.fr
