M2 internship: Dissecting the spatial patterning of soil eDNA across spatial scales and organisms.

Titre du stage : Dissecting the spatial patterning of soil eDNA across spatial scales and organisms.

Structure d’accueil:
Option 1 : Équipe DEEP – UMR 5300 CRBE (Centre de Recherche sur la Biodiversité et l’Environnement), Toulouse.
Option 2 : UMR EcoFoG – Écologie des Forêts de Guyane, Kourou, Guyane Française.

Responsables du stage :
Lucie ZINGER (MCF détachée). Contact : lucie@zinger.fr . Website: https://luciezinger.wordpress.com/
Jérémy RAYNAUD (Doctorant). Contact : jeremy.raynaud@univ-tlse3.fr
Irene CALDERON-SANOU (MCF). Contact : irene.calderon-sanou@univ-guyane.fr

Description du stage :
Environmental DNA-based techniques, in particular eDNA metabarcoding, have recently revolutionized the way we study soil biodiversity by enabling more comprehensive and efficient sampling of the soil biota. By extracting and analyzing DNA directly from soil samples, it is now possible to study simultaneously all components of soil food webs, ranging from microbes to arthropods and plants, and this at larger spatial scales and with greater precision than ever before. This breakthrough has opened new avenues for basic research (e.g. identifying key stressors of the soil biota, of its resilience, etc.) and more applied applications (e.g. biomonitoring of polluted or protected/restored areas). However, while significant advances have been made in eDNA metabarcoding molecular and bioinformatics protocols, the field sampling design remains a crucial yet often overlooked aspect. This aspect is even more important as we are now gathering an increasing number of multi-taxa inventories encompassing organisms differing, amongst other things, in body size by several orders of magnitude, and thus in the way they distribute spatially in the environment.
The internship will aim to investigate the spatial behavior of the soil eDNA signal describing plant, soil fauna, and soil microbial diversity. It will rely on a database of existing soil DNA metabarcoding-based inventories conducted in 1 to 12 ha forest plots located in different regions (e.g. Colombia, Poland, French Guiana, etc.), exhibiting regionally different types of environmental gradients (e.g. soil condition, altitude, land use change, etc.), generated using different markers (16S, 18S, ITS, trnL, mt 16S, etc. depending on the study location) and spatial sampling protocols. Several metadata characterizing the local environmental gradient are also available.
After bioinformatics treatment of the data (i.e. data size reduction, PCR/sequencing noise or contaminants removal, taxonomic annotation), the student will compare how alpha and beta diversity varies spatially and along environmental gradients using different levels of data spatial aggregation (either through differences of sampling design per se or through in silico data spatial aggregation). More specifically, the student will measure the inter vs. intra-plot diversity/compositional spatial variability for each focal clade and/or body size class and at different spatial grain. Diversity patterns predictability by spatial variables or environmental gradients will be then determined across spatial grains and organisms clades/body size classes and used to identify optimal clade-specific or multi-taxa sampling strategies.
This internship offers a unique opportunity to contribute to cutting-edge research in eDNA research. The student will gain valuable experience in analysis of multi-taxa eDNA-based data in general and for the study belowground biodiversity, as well as in spatial ecology, by mobilizing the principles of spatial scales and autocorrelation. By addressing the critical aspect of sampling design, this project will contribute to the development of more effective and informative eDNA-based studies.

Planned schedule :
– janvier: Gathering and formatting of the sequencing data and associated metadata
– fev-april: Analyses of eDNA spatial patterns and predictability across markers/clades/body sizes.
– may-june : Thesis writing.

Starting date and duration:
Early 2025 (flexible dates), duration of 4 to 6 months.

Relevant articles for the project:
Averill, C., Werbin, Z. R., Atherton, K. F., Bhatnagar, J. M., & Dietze, M. C. (2021). Soil microbiome predictability increases with spatial and taxonomic scale. Nature Ecology & Evolution, 5(6), 747-756.
Blackman, R., Couton, M., Keck, F., Kirschner, D., Carraro, L., Cereghetti, E., … & Altermatt, F. (2024). Environmental DNA: The next chapter. Molecular Ecology, 33(11), e17355.
Chalmandrier, L., Pansu, J., Zinger, L., Boyer, F., Coissac, E., Génin, A., … & Thuiller, W. (2019). Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales. Ecography, 42(12), 2144-2156.
Dickie, I. A., Boyer, S., Buckley, H. L., Duncan, R. P., Gardner, P. P., Hogg, I. D., … & Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA‐based studies. Molecular Ecology Resources, 18(5), 940-952.
Estes, L., Elsen, P. R., Treuer, T., Ahmed, L., Caylor, K., Chang, J., … & Ellis, E. C. (2018). The spatial and temporal domains of modern ecology. Nature ecology & evolution, 2(5), 819-826.
Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For biodiversity research and monitoring. Oxford University Press.
Zinger, L., Taberlet, P., Schimann, H., Bonin, A., Boyer, F., De Barba, M., … & Chave, J. (2019). Body size determines soil community assembly in a tropical forest. Molecular Ecology, 28(3), 528-543.
Zinger, L., Bonin, A., Alsos, I. G., Bálint, M., Bik, H., Boyer, F., … & Taberlet, P. (2019). DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Molecular ecology, 28(8), 1857-1862.