PhD project offered by the IMPRS-gBGC in July 2025

Decoding Groundwater Ecosystem Functions through Multi-Omics: Impacts of Geology and Weather Extremes in the Subsurface Critical Zone

Kirsten Küsel, Gerd Gleixner

Project description

The terrestrial Critical Zone (CZ)—extending from the vegetation canopy through soils and aquifers—hosts a multitude of tightly coupled physical, chemical, and biological processes (Brantley et al., 2017). Within this complex system, groundwater ecosystems play a vital but often overlooked role in mediating biogeochemical cycling, sustaining water quality, and hosting diverse microbial life (Roth et al., 2019; Spracklen et al., 2018; Wegner et al., 2019). However, the influence of geological setting on subsurface microbiomes and their role in ecosystem functioning remains poorly understood, particularly under conditions of environmental stress such as weather extremes which can affect groundwater quality (Schroeter et al., 2024).

This PhD project will leverage the extensive infrastructure and long-term datasets of the Collaborative Research Center AquaDiva, specifically focusing on the Hainich Critical Zone Exploratory (CZE) and the Saale-Elster-Observatory (SESO). These contrasting field sites offer unique opportunities to investigate the links between geological heterogeneity, microbial community structure, and biogeochemical processes in groundwater systems.

In March 2025, an unprecedented multi-omics campaign was conducted across AquaDiva field sites, generating a rich dataset that includes:

Metagenomes, metatranscriptomes, proteomes, and metabolomes
High-resolution characterization of dissolved organic matter (DOM)

In addition, we have a 12-year time-series data of bacterial 16S rRNA amplicons, combined with long-term hydrochemical and DOM profiles (Wang et al., 2025). These data provide a unique opportunity to unravel how subsurface microbial communities respond to geological setting, hydrogeochemical gradients, and weather extremes-induced disturbances such as droughts followed by intense precipitation events.

Research Objectives and Questions

The central objective of this PhD project is to analyze and integrate multi-omics and DOM datasets to identify microbial and molecular signatures that reflect ecosystem functioning and vulnerability in contrasting groundwater systems.

The project will address the following key questions:

How does geological heterogeneity (e.g., rock type) shape microbial community composition and function in groundwater ecosystems?
What are the major drivers linking microbial diversity, gene expression, and metabolite profiles across time and space?
How do weather extremes (e.g., heavy rainfall following drought) affect the connectivity between surface and subsurface zones, and how is this reflected in microbial community shifts and DOM signatures?
Can we identify bioindicators or functional traits that signal ecosystem vulnerability or resilience in the face of environmental change?

Approach and Methodology

The PhD candidate will work with an interdisciplinary team to process and integrate high-dimensional biological and geochemical datasets. Core methods will include:

Amplicon sequencing (16S rRNA gene) to track microbial taxonomic shifts over time
Shotgun metagenomics and MAG reconstruction to explore functional potential
Metatranscriptomics and proteomics to assess active metabolic pathways
Metabolomics and DOM characterization to evaluate biochemical signatures and carbon processing
Multivariate and network-based data integration techniques to identify cross-omics patterns and links to hydrochemical parameters

The project will benefit from the candidate’s close collaboration with teams working on DOM chemistry and meta-omic analyses as part of the broader Microverse research effort of the excellence Cluster: "Balance of the Microverse".

Environment and Supervision

The PhD project will be embedded in the International Max Planck Research School for Global Biogeochemical Cycles (IMPRS-gBGC) and conducted in close collaboration with the Max Planck Institute for Biogeochemistry, Friedrich Schiller University Jena, former partners of the CRC AquaDiva, and PIs of the Excellence Cluster Balance of the Microverse. The candidate will join a dynamic, interdisciplinary research environment with access to state-of-the-art omics and geochemical laboratories, computational infrastructure, and field observatories.

Affiliation and support

The PhD candidate will be affiliated to the chair "Aquatic Geomicrobiology" at the Institute for Biodiversity, Ecology and Evolution at FSU Jena and the "Molecular Biogeochemistry" group at MPI-BGC. The successful PhD candidate jointly work with other PhD candidates on the project, which will most likely enhance the impact of this research project.

Requirements

Applications to the IMPRS-gBGC are open to well-motivated and highly-qualified students from all countries. For this particular PhD project we seek a candidate with

a Master’s degree in Biology, Microbiology or other related sciences, such as Environmental Sciences/ Agriculture with special focus on molecular biology
experience in 16S rRNA amplicon sequencing, metagenomic analyses, bioinformatics and handling of big data sets
of advantage is experience multivariate analysis
very good oral and written communication skills in English

The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. It is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

References

Brantley, S. L., McDowell, W. H., Dietrich, W. E., White, T. S., Kumar, P., Anderson, S. P., et al. (2017). Designing a network of critical zone observatories to explore the living skin of the terrestrial Earth. Earth Surface Dynamics, 5, 841–860. https://doi.org/10.5194/esurf-5-841-2017

Roth, V.-N., Lange, M., Simon, C., Hertkorn, N., Bucher, S., Goodall, T., et al. (2019). Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nature Geoscience, 12, 755–761. https://doi.org/10.1038/s41561-019-0417-4

Schroeter, S. A., Orme, A. M., Lehmann, K., Lehmann, R., Chaudhari, N. M., Küsel, K., ..., Gleixner, G. (2025). Hydroclimatic extremes threaten groundwater quality and stability. Nature Communications, 16(1), 720.

Spracklen, D. V., Baker, J. C. A., Garcia-Carreras, L., Marsham, J. H. (2018). The Effects of Tropical Vegetation on Rainfall. Annual Review of Environment and Resources, 43(1), 193–218. https://doi.org/10.1146/annurev-environ-102017-030136

Wang, H., Herrmann, M., Schroeter, S.A., Zerfaß, C., Lehmann, R., Lehmann, K., Ivanova, A., Pohnert, G., Gleixner, G., Trumbore, S.E. and Totsche, K.U., 2025. Balancing Act: Groundwater microbiome"s resilience and vulnerability to hydroclimatic extremes. bioRxiv, pp.2025-02.

Wegner, C.E., Gaspar, M., Geesink, P., Herrmann, M., Marz, M. and Küsel, K. (2019). Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Applied and environmental microbiology, 85(5), pp.e02346-18.

left: Groundwater sampling at the Hainich CZE (© Falko Gutmann), right: High-volume groundwater filtration (© Johann Carl)