PhD project offered by the IMPRS-gBGC in Jan 2024

What can new organic markers reveal about the seasonal metabolism of the tropical critical zone?

Gerd Gleixner , Thorsten Schäfer , Carsten Simon , Eliane Gomes-Alves , Sam Jones , Carlos Quesada , Savio Ferreira

Project description

Forest ecosystems are part of the Critical Zone, which reaches from the lower troposphere to the rivers, soils and aquifers of the Earth’s near surface and encompasses the whole terrestrial biosphere (Brantley et al., 2017). This zone is deemed “critical” because it represents the major interface where crucial biogeochemical processes of water (retention in soil, formation of rain) and carbon cycling (nutrient remineralization, C sequestration, photosynthesis and growth) take place (Roth et al., 2019; Spracklen et al., 2018). Volatile and dissolved or colloidal organic molecules are important ecological and biochemical signals (“biomarkers”) that mediate and reflect these processes (Bourtsoukidis et al., 2018; Malik et al., 2020; Roth et al., 2019), and play a significant role in the distribution of nutrients and trace elements (Kretzschmar & Schäfer, 2005; Yan et al., 2014). However, these processes are little understood, especially in ecosystems like ultra-diverse Amazonian forests that contain exceptionally poor soils but large biomass (Fleischer et al., 2019; Lugli et al., 2019). Novel organic markers could thus improve our understanding of fundamental processes such as soil organic matter decomposition and how they sustain ecosystem productivity.

The Amazon is the largest of all tropical forests, and ranks among the most productive and diverse biomes globally (Malhi, 2012). Despite its major role in Earth’s climate system, the Amazon is under threat from deforestation and changing climatic conditions (Drake et al., 2019). To predict responses of the forest and to ultimately preserve it, we need to understand the functioning of these systems in their undisturbed state. Better understanding may be aided by recent technology that allows us to study unknown metabolic signals in unprecedented detail, e.g. by ultrahigh resolution mass spectrometry (FT-MS; Simon et al., 2018), proton transfer reaction mass spectrometry (PTR-MS; Peacock et al., 2018), and liquid chromatography coupled to organic carbon and organic nitrogen detection (LC-OCD-OND; Huber et al., 2011). Concentrations of trace elements in dissolved or colloidal organics can be determined by inductively coupled plasma mass spectrometry (ICP-MS; Simon et al., 2019).
Within this IMPRS project, the candidate will build upon a collaboration between the Max Planck Institute for Biogeochemistry, the Friedrich Schiller University Jena and the National Institute of Amazon Research (INPA) in Manaus, Brazil. Field work will be focused on two research stations located in the Cuieiras reserve (within the Large-Scale Biosphere-Atmosphere program focusing on a newly established FACE Experiment and the Uatumã reserve (within the Amazon Tall Tower Observatory program)). The project combines extended periods of field work in pristine tropical forest systems with the use of modern analytical tools.

Research aim & questions

The overall research aim is to analyze temporal data of molecular signals and to relate it to key environmental variables such as temperature, precipitation, soil texture, and water solution chemistry (pH, electrical conductivity, C concentrations). The research centers around the following questions: How is the nutrient limitation of the ecosystem mirrored in dissolved organic molecules? Which organic molecules are labelled by the plant derived carbon in the FACE experiment? How is drought impacting carbon and nutrient cycling? For this, the candidate will work with data from different forest types, using networks of lysimeters and piezometers that span from most diverse terra firme rainforests to low diversity white-sand Campina forests. Thereby, the PhD project will link ecosystem properties and environmental drivers to the metabolic responses of major tropical forest types under the extremes of seasonal climatic variability. Thereby, the project will help to understand how tropical forests, soils, and climate interact on a molecular level, and will increase our knowledge of key markers that may allow future monitoring and thus preservation of these important ecosystems.

Applied techniques

Within the project, advanced analytical techniques, such as FT-MS, PTR-MS and LC-IRMS, will be used to analyze patterns and trends of metabolic responses. Sophisticated data processing techniques, such as time series analysis and multivariate analysis will be applied to discern markers of “usual” seasonality and those of extremes such as rewetting events after prolonged drought, which may ultimately serve as new “warning signals” of tropical forest functioning under global change.

Affiliation and support

The PhD candidate will be affiliated to the chair “Applied Geology” at the Institute for Geosciences at FSU Jena and the “Molecular Biogeochemistry” group at MPI-BGC and will visit Manaus to conduct field work. The successful PhD candidate will analyse the molecular and isotopic properties of water samples from soils and streams using Orbitrap FT-MS and LC-IRMS techniques, and PTR-MS can be applied to study the gas-phase transfer from soils to the atmosphere. LC-OCD-OND and ICP-MS can be further applied for the characterization of environmental colloids in soil solution. Supervision at the FSU Jena is provided by Prof. Dr. Thorsten Schäfer, and by Prof. Dr. Gerd Gleixner at MPI-BGC. Additional support will come from Dr. Carsten Simon (DOM characterisation by Orbitrap MS at MPI Jena), Dr. Eliane Gomes-Alves and Dr. Sam Jones (Gas-phase molecular analyses at MPI Jena and INPA, Manaus), and Dr. Alberto Quesada and Dr. Savio Ferreira (Soil and hydrological laboratories at INPA in Manaus).

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 Chemistry, Environmental Chemistry or other chemistry related sciences, such as Environmental Sciences/ Forestry with special focus on Geochemistry
Experience in analytical chemistry, especially mass spectrometry, and handling of big data sets
Of advantage is experience in FT-MS techniques (TOF, FT-ICR-MS or Orbitrap)
Of advantage is experience in time series analysis or multivariate analysis
Of advantage are oral communication skills in Portuguese
Very good oral and written communication skills in English

The Max Planck Society (MPS) strives for gender equality and diversity. The MPS aims to increase the proportion of women in areas where they are underrepresented. Women are therefore explicitly encouraged to apply. We welcome applications from all fields. The Max Planck Society has set itself the goal of employing more severely disabled people. Applications from severely disabled persons are expressly encouraged.

References

Bourtsoukidis, E., Behrendt, T., Yañez-Serrano, A. M., Hellén, H., Diamantopoulos, E., Catão, E., et al. (2018). Strong sesquiterpene emissions from Amazonian soils. Nature Communications, 9, 2226. https://doi.org/10.1038/s41467-018-04658-y
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
Drake, T. W., Van Oost, K., Barthel, M., Bauters, M., Hoyt, A. M., Podgorski, D. C., et al. (2019). Mobilization of aged and biolabile soil carbon by tropical deforestation. Nature Geoscience, 12, 541–546. https://doi.org/10.1038/s41561-019-0384-9
Fleischer, K., Rammig, A., De Kauwe, M. G., Walker, A. P., Domingues, T. F., Fuchslueger, L., et al. (2019). Amazon forest response to CO₂ fertilization dependent on plant phosphorus acquisition. Nature Geoscience, 12, 736–741. https://doi.org/10.1038/s41561-019-0404-9
Huber, S. A., Balz, A., Abert, M., & Pronk, W. (2011). Characterisation of aquatic humic and non-humic matter with size-exclusion chromatography - organic carbon detection - organic nitrogen detection (LC-OCD-OND). Water Research, 45, 879–885. https://doi.org/10.1016/j.watres.2010.09.023
Kretzschmar, R., & Schäfer, T. (2005). Metal Retention and Transport on Colloidal Particles in the Environment. Elements, 1, 205–210. https://doi.org/10.2113/gselements.1.4.205
Lugli, L. F., Andersen, K. M., Aragão, L. E. O. C., Cordeiro, A. L., Cunha, H. F. V., Fuchslueger, L., et al. (2019). Multiple phosphorus acquisition strategies adopted by fine roots in low-fertility soils in Central Amazonia. Plant and Soil, 450, 1–15. https://doi.org/10.1007/s11104-019-03963-9
Malhi, Y. (2012). The productivity, metabolism and carbon cycle of tropical forest vegetation. Journal of Ecology, 100, 65–75. https://doi.org/10.1111/j.1365-2745.2011.01916.x
Malik, A. A., Swenson, T., Weihe, C., Morrison, E. W., Martiny, J. B. H., Brodie, E. L., et al. (2020). Drought and plant litter chemistry alter microbial gene expression and metabolite production. ISME Journal. https://doi.org/10.1038/s41396-020-0683-6
Peacock, M., Materic, D., Kothawala, D. N., Holzinger, R., & Futter, M. N. (2018). Understanding Dissolved Organic Matter Reactivity and Composition in Lakes and Streams Using Proton-Transfer-Reaction Mass Spectrometry (PTR-MS). Environmental Science and Technology Letters, 5, 739–744. https://doi.org/10.1021/acs.estlett.8b00529
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
Simon, C., Roth, V.-N., Dittmar, T., & Gleixner, G. (2018). Molecular Signals of Heterogeneous Terrestrial Environments Identified in Dissolved Organic Matter: A Comparative Analysis of Orbitrap and Ion Cyclotron Resonance Mass Spectrometers. Frontiers in Earth Science, 6, 1–16. https://doi.org/10.3389/feart.2018.00138
Simon, C., Osterholz, H., Koschinsky, A., & Dittmar, T. (2019). Riverine mixing at the molecular scale – An ultrahigh-resolution mass spectrometry study on dissolved organic matter and selected metals in the Amazon confluence zone (Manaus, Brazil). Organic Geochemistry, 129, 45–62. https://doi.org/10.1016/j.orggeochem.2019.01.013
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
Yan, M., Korshin, G. V., Claret, F., Croué, J. P., Fabbricino, M., Gallard, H., et al. (2014). Effects of charging on the chromophores of dissolved organic matter from the Rio Negro basin. Water Research, 59, 154–164. https://doi.org/10.1016/j.watres.2014.03.044

Studying the seasonal metabolism of the tropical critical zone by novel molecular markers: (a - e) Schematic landscape section of different forests and their topsoil (up to ~ 40 cm depth) at the ATTO site; (f – i) DOM fingerprints assessed by Orbitrap mass spectrometry, in usual displays as mass spectrum (left panels) and Van Krevelen plots (right panels); (j) View of the central 325m tower at the Amazon Tall Tower Observatory (ATTO; © Jost Lavric, MPI-BGC); (k) Front view of the LC-Orbitrap Elite MS system at MPI-BGC Jena; (l) DOC time series from lysimeters at a terra firme forest site (soil profile shown in b) installed in 5 and 30 cm soil depth, with a pronounced drought from August to November 2018; (m) Depth trends in DOC concentration across all time points and depths at the same site (b).