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Job advertisement PhD project: What can new organic markers reveal about the seasonal metabolism of the tropical critical zone?

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

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

International Max Planck Research School for Global Biogeochemical Cycles logo

International Max Planck Research School for Global Biogeochemical Cycles

In cooperation with the Friedrich Schiller University Jena, the Max Planck Institute for Biogeochemistry houses a unique and flexible research program that grants German and foreign students a broad selection of learning opportunities while still maintaining a research focus. The IMPRS-gBGC offers a PhD program specializing in global biogeochemistry and related Earth system sciences. The overall research and teaching focuses on:

  • Improved understanding of biogeochemical processes with an emphasis on terrestrial ecosystems
  • Development of observational techniques to monitor and assess biogeochemical feedbacks in the Earth system
  • Theory and model development for improving the representation of biogeochemical processes in comprehensive Earth system models


Jena, Germany


Relevant divisions
Biogeosciences (BG)
Climate: Past, Present & Future (CL)
Soil System Sciences (SSS)

Full time

Student / Graduate / Internship

We offer scholarships for 4 years and full-time contracts for 3 years within an international and multidisciplinary working environment. The starting date is flexible.

Preferred education

Application deadline
16 August 2022

24 June 2022

Job description

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

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) 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 (Fig. 1).

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 do molecular signals vary seasonally?
  • How are they affected by precipitation and drought events?
  • Which markers are indicative of ecosystem-specific processes, and can we track these signals in local streams and rivers?

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 and PTR-MS, 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 properties of water samples from soils and streams using Orbitrap FT-MS 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 ETH Zurich), Dr. Eliane Gomes-Alves and Dr. Sam Jones (Gas-phase molecular analyses at MPI Jena), and Dr. Alberto Quesada and Dr. Savio Ferreira (Soil and hydrological laboratories at INPA in Manaus).


First and foremost we seek a person with strong scientific curiosity from all countries! We would give preference to a person 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 seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

How to apply

Apply online on until August 16, 2022.