PhD student in biogeochemistry

The Department of Ecology and Genetics is an international environment with staff and students from all over the world. Our research spans from evolutionary ecology and genetics to ecosystem studies. Learn more at www.ieg.uu.se.

We are now looking for a PhD student in biogeochemistry to the Limnology program.

Limnology program. Limnology is the study of inland water ecosystems, including interactions of communities and populations, organisms ranging from microorganisms to predatory fish and the biogeochemical cycling of nutrients. The limnology program includes research on fundamental scientific questions, as well as applied topics of concern for the protection and management of the aquatic environment. The program includes three major research groups, which have a considerable amount of synergy and cooperation between them, including aquatic communities and populations, microbial ecology and biogeochemistry. This position fits well with strong connections to biogeochemistry and microbial ecology research groups.

The biogeochemistry group. A large share of our research addresses the reactivity of organic matter: to which extent is organic matter degraded by microbes into carbon dioxide or methane, and why? Under which circumstances does organic matter escape microbial attack? We study both dissolved organic matter in the water column and particulate organic matter in lake sediments, terrestrial soils and marine ecosystems. We approach these questions with experiments ranging from the micro-scale to mesocosms, with field campaigns and regional and global data syntheses.

Read more about the limnology program here.

Read more about the biogeochemistry group here.

Project description
This PhD project is part of a project funded by the Swedish National Science Foundation: Linking Functionally Relevant Characteristics of Dissolved Organic Matter (DOM) to Functional Traits of the Microbial Community (Fun-DOM). The project focuses on unravelling functionally relevant characteristics of DOM and linking them to microbial uptake.

Overview. Most living biomass across the biosphere is comprised of organic matter (OM) that is 50% carbon-based. When decomposing in a liquid state as dissolved organic matter (DOM), it can pass across biological membranes and is a vital source of energy recycled back to living biomass. When degraded by aerobic microbes, DOM produces atmospheric CO2, a greenhouse gas contributing to global warming. The amount of time it takes for DOM to degrade is highly variable, spanning from minutes to millennia, and remains perplexing to predict. The uncertainty associated with predicting rates of DOM degradation remains one of the greatest barriers to projecting how the global carbon cycle might change in the future. Thus, an unresolved question central to biogeochemistry is: What controls the rate of DOM degradation? This PhD project aims to link functionally relevant characteristics of DOM to functional traits of the microbial community under variable kinetic scenarios. While the project will be conducted within a limnology program, the questions we ask in this project are relevant to freshwater, soil and marine ecosystems. The project aims to develop highly technical chemical and biological approaches to answer ecologically meaningful questions. The chemical and biological approaches are described briefly below.

The chemical approach. Within a single water sample containing DOM, there are several hundred thousand organic compounds that can be identified using high-resolution mass spectrometry. High-resolution mass spectrometry can provide the elemental composition (C:H:O:N:S:P) of these organic compounds. However, there is limited information about structural characteristics or functional group configuration. The project will strive to develop new chemometric methods to interpret data derived from mass spectrometry to help identify functionally relevant characteristics of DOM.

The biological approach. Another goal of this project is the identification of genome-resolved functional genes involved in enzymatic degradation. Genome-resolved metagenomics is a rapidly progressing field, particularly developing pipelines for bioinformatic analysis, functional gene annotation, and gene-resolved metatranscriptome analyses. To track the role of microbes in degrading different DOM compounds, we will combine metagenomics to construct the genome and metatranscriptomics to track changes to gene i.e. the production of enzymes).

What we offer you. You will be provided with training to use and develop technical tools, including programming and lab skills, as well as other skills, such as time management, stress management and scientific writing. The project's success will be facilitated by support from two co-supervisors with complementary expertise in the chemical analysis of DOM (Dolly Kothawala, Limnology, UU) and aquatic microbes and bioinformatics (Maliheh Mehrshad at the nearby Swedish University of Agricultural Sciences). The limnology program and research groups you will work most closely with are interdisciplinary and international. We will have regular face-to-face supervision meetings with regular check-ups on you and your project, including your well-being and mental health. We have regular social events to promote a supportive, healthy workplace environment. We encourage PhD students to have a healthy lifestyle balancing work and life and try to promote a secure support network for all researchers to thrive, be creative and reach their highest potential.

Duties
As a PhD student specializing in biogeochemistry, you will participate in the limnology program within a group focusing on biogeochemistry and the cycling of organic matter. You will design and carry out laboratory experiments. You will interpret complex biological and chemical data with existing programming tools. In addition, you will develop new programming tools as needed to analyze chemical and biological data. In addition to your research, there will be teaching and other administrative activities within the limnology program. The teaching and other administrative duties can add up to 20% of the working hours.

Qualifications required
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in the areas of biology, chemistry and/or engineering, or
• have completed at least 240 credits in higher education with at least 60 credits at Master’s level, including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

We attach great importance to personal qualities such as creativity, flexibility, taking the initiative when opportunities arise, problem-solving, perseverance, working collaboratively, verbal and written expression, contributing to a positive working environment and stress management. Candidates must be able to express themselves fluently in spoken as well as written English.

Qualifications desired
Knowledge in biology, chemistry and/or engineering with experience using programming tools are highly desired qualifications for the position. Competencies that are desirable but not mandatory include courses in ecology, limnology, biochemistry, analytical chemistry and/or organic chemistry. The candidate should already be familiar with programming tools and be willing to advance these skills to an advanced level.

We are looking for a highly motivated candidate who is curious to learn about the natural environment and, at the same time, can multi-task and work with highly technical components of a project.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 §7. Scope of employment: full-time. Starting date 2025-09-01, or as agreed. Placement: Uppsala.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

For further information about the position, please contact
Dolly Kothawala (Limnology program, Department of Ecology and Genetics, Uppsala University), dolly.kothawala@ebc.uu.se, or Maliheh Mershad (Division of Microbial Ecology, Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences) maliheh.mehrshad@slu.se.

Application instructions
The application should include 1) a letter describing yourself, your research interests, why you want to pursue a Ph.D., and why you are suitable for the position, 2) your CV, 3) a brief description of your education, including the courses you have taken that are relevant for this position, 4) a copy of your master's degree and your course grades, along with a copy of your master's thesis, 5) names and contact details of at least two referees (email addresses and phone numbers), and 6) any publications if applicable. The application should be written in English.

You are welcome to submit your application no later than May 30, 2025. UFV-PA 2025/898.

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